The Pakistan Navy (PN) (Urdu: پاکستان بحریہ; romanized: Pākistān Bahrí'a; pronounced [ˈpaːkɪstaːn baɦɽia]) is the naval warfare branch of the Pakistan Armed Forces. The Chief of the Naval Staff, a four-star admiral commands the navy. The Pakistan Navy operates on the coastline of Pakistan in the Arabian Sea and Gulf of Oman. It was established in August 1947, following the independence of Pakistan from the United Kingdom.

The primary role of the Pakistan Navy is to defend Pakistan's sea frontiers from any external enemy attack. In addition to its war services, the Navy has mobilized its war assets to conduct humanitarian rescue operations at home as well as participating in multinational task forces mandated by the United Nations to prevent seaborne terrorism and piracy off the coasts.

The Pakistan Navy is a volunteer force which has been in conflict with neighbouring India twice on its sea borders, and has been repeatedly deployed in the Indian Ocean to act as a military advisor to Gulf Arab states and other friendly nations during the events of multinational conflict as part of its commitment to the United Nations. The Navy has several components including the Naval Aviation, Marines, and the Maritime Security Agency (a coast guard). Since its commencement on 14 August 1947, the defensive role of the Navy has expanded from securing the sealines and becoming the custodian of Pakistan's second strike capability with an ability to launch underwater missile system to target enemy positions.

The Navy is commanded by the Chief of the Naval Staff, a four-star admiral and also known as (Urdu: امیر البحر; romanized who is a member of the Joint Chiefs of Staff Committee. The Chief of Naval Staff is nominated by the Prime Minister and appointed by the President of Pakistan. The current Chief is Admiral Naveed Ashraf who was appointed on 7 October 2023. Admiral Naveed Ashraf is the 23rd Chief of the Pakistan Navy, taking charge after Muhammad Amjad Khan Niazi.

Today is a historic day for Pakistan, doubly so for those of us in the Navy. The Dominion of Pakistan has come into being and with it a new Navy – the Royal Pakistan Navy – has been born. I am proud to have been appointed to command it and serve with you at this time. In the coming months, it will be my duty and yours to build up our Navy into a happy and efficient force

— Muhammad Ali Jinnah, the founder of Pakistan, addressing the men and officers of HMIS Godavari in March 1948

The Pakistan Navy came into existence on 15 August 1947 with the establishment of Pakistan as an independent state from the United Kingdom. The Armed Forces Reconstitution Committee (AFRC), under Field Marshal Sir Claude Auchinleck, the last British Commander-in-Chief, India (C-in-C, India), divided the shares and assets of the Royal Indian Navy (RIN) between India and Pakistan in a ratio of 2:1, with Pakistan receiving the two sloops, two frigates, four minesweepers, two naval trawlers and four harbour launches. The Armed Forces Reconstitution Committee (AFRC) allocated about two-thirds of the assets of the Royal Indian Navy to India while one third was given to the new Dominion of Pakistan, despite Pakistan having inherited the high percentage of delta areas on its coast and the large maritime area covering the Arabian sea on the West and the Bay of Bengal on the East. In addition, India also objected to transfer any machinery at the Bombay Dockyard to Pakistan and further refused to part the machinery that happened to be on its soil.

The Navy endured a difficult history— with only 200 officers and 3,000 sailors were inherited to the Navy – the most senior being Captain HMS Choudri who had little experience in the military staffing. Of the ~200 officers, twenty of these had come from the Executive Branch of the Royal Indian Navy, and only six officers were the mechanical engineers while there were none electrical engineers or specialists to care for the electrical systems needed to be look after in the weapons systems or the powering up the machinery in the vessels as whole. The Navy suffered perennial problems with inadequate staff, lack of operational bases, lack of financial support, and poor technological and personnel resources. Secondly, it grew out as the smallest military uniform branch that contributed in its lack of importance in federal budgets as well as the problems relating to its institutional infrastructure.

The Army and the Air Force were the dominant forces where the defence planning were based wholly on army and air force point of view. Additional problems relating to the Navy were the lack of facilities and maintenance machinery, as the only naval dockyard on the subcontinent was located in Bombay in India.

To overcome these difficulties, the Navy had to launch a recruitment programme for the young nation, starting in East Pakistan which proved to be very difficult to sustain the programme; therefore, it was moved back to West Pakistan to concentrate recruitment on West Pakistan. Furthermore, the Navy's procurement was greatly determined by its war role and it had to struggle for a role for itself throughout its history from its beginning.

The Navy's combat actions largely remained in absence during the first war with India in 1947–48 as all the fighting was restricted to land and aerial combat missions. On operational planning, Captain HMS Choudri had engaged on commanding a former RIN destroyer from Karachi to Bombay to oversee the evacuation of Indian emigrants to Pakistan. In 1948, the Royal Pakistan Navy had to engage in humanitarian missions to evacuate Indian immigrants trapped in disputed and hostile areas, with its frigates operating continuously.

Command and control of the new Royal Pakistan Navy was extremely difficult as Prime Minister Liaquat Ali Khan's administration had to extend the employment of a large number of the Royal Navy officers from the British Admiralty, with Rear Admiral James Wilfred Jefford, RN, appointed as the Flag Officer Commanding (FOC) who worked on creating the contingency plan, "Short-term Emergency Plan (STEP)", to work up the frigates and naval defences in case of escalation of the war at sea. In 1948, the Directorate-General for the Naval Intelligence (DGNI), a staff corps, was established under Lieutenant S. M. Ahsan, who served as its first Director-General, in Karachi. When the first war came to an end in 1948, the Navy temporarily established its Navy NHQ in Karachi and acquired its first O-class destroyer from the transfer by the Royal Navy.

The Royal Pakistan Navy greatly depended on the generous donations from the British Royal Navy with two Battle-class destroyers, PNS Tippu Sultan and PNS Tariq. Tippu Sultan was commissioned on 30 September 1949, under Commander P.S. Evans, whilst Tariq was placed under the command of Lieutenant-Commander A. R. Khan. The two destroyers formed the 25th Destroyer Squadron, as PNS Jhelum and PNS Tughril, under Commander Muzaffar Hasan, also joined the Royal Pakistan Navy.

In 1950, the Navy's nationalisation took place when many officers from the air force and army volunteered to join the navy and NCOs gaining commission as an officers. Support from the army and air force to the navy led to the establishment of logistics and maintenance machinery with vigorous efforts directed towards integrating the navy presence in East Pakistan, thereby creating opportunities for people in East Pakistan to participate in the build-up.

In 1951, the Pakistan government called for appointing native chiefs of the armed forces, but it was not until 1953 that a native navy chief was appointed. The British Admiralty, however, maintained the command of the Navy through Rear-Admiral Jefford who had native deputy chiefs of staff including Commodore HMS Choudhri, Commodore Khalid Jamil, and Commander M.A. Alavi.

During this time, a number of goodwill missions were carried out by the navy's warships, and non-combat missions were conducted under the auspices of the Royal Navy. In 1951, HMS Choudhri's promotion papers as naval chief were approved by Prime Minister Liaquat Ali Khan but it was not until 1953 when HMS Choudhri was promoted as vice admiral and commander with the support from army commander-in-chief General Ayub Khan. He handed over the command of 25th Destroyer squadron to a Polish naval officer, Commander Romuald Nalecz-Tyminski.

In the mid-1950s, the Ministry of Finance awarded contracts to the Corps of Engineers (Pakistan Army) for the construction of the Karachi Naval Dockyard. In 1954, several efforts were made to procure a Ch-class submarine from the Royal Navy but was rejected by British Admiralty which agreed to loan the Ch-class destroyer, HMS Chivalrous, which was renamed PNS Taimur. From 1953 to 1956, HMS Choudri bitterly negotiated with the United States over the modernisation of the navy and convinced the U.S. government to provide monetary support for modernisation of ageing O–class destroyers and minesweepers, while commissioning the Ch–class destroyers from the Royal Navy. British naval tradition was disbanded and cancelled when the United States Navy's advisers were dispatched to the Pakistani military in 1955.

With the promulgation of the Constitution of Pakistan that established the republicanism featuring the federalised government, the prefix Royal was dropped, and the service was re-designated the Pakistan Navy ("PN") with the Jack replaced the Queen's colour and the White Ensign respectively in 1956. The order of precedence of the three services changed from Navy–Army–Air force to Army–Navy–Air Force.

In February 1956, the British government announced the transfer of several major surface combat warships to Pakistan Navy, including a cruiser and four destroyers to be purchased with funds made available under the U.S. Military Assistance Program. In 1957, the Navy finalised the purchase of a cruiser from the United Kingdom and used the government's own funds for the purchase which caused a great ire against Admiral Choudhri in the Finance Ministry.

In 1958, the Navy made an unsuccessful attempt to obtain Neptun-class submarines from Sweden using the American security funds; it was halted by the United States and Pakistan's Finance Ministry despite the fact that the idea had support from Army GHQ. In 1958–59, the Navy NHQ staff began quarrelling with the Army GHQ staff and the Ministry of Defense (MoD) over plans regarding the modernisation of the navy that resulted in bitter interservice rivalry between army and navy and ended with Admiral Choudri's resignation to the Presidency in 1959.

Proposal of attaining the aircraft carrier was deferred due to financial constraints, forcing Pakistan to move towards establishing the formidable submarine command. From 1956 to 1963, two destroyers, eight coastal minesweepers, and an oiler were procured from the United States and United Kingdom as a direct result of Pakistan's participation in the anti-Communist defence pacts SEATO and CENTO.

After the bitter resignation of Vice-Admiral HMS Choudri in 1959, Vice-Admiral Afzal Rahman Khan was appointed as the Commander in Chief in Navy who worked towards building relations with President Ayub Khan in retaining hopes for procuring a submarine despite financial constraints. The Royal Navy accepted the long awaiting requests from the Pakistan Navy for a regular visit to Karachi Naval Dockyard to provide first hand experience in submarine operations in 1960–61. The Ayub administration did not increase the financial funding of the navy at the expense to army and air force but he did not object to American contributions to train the Pakistan Navy in submarine operations. It was the U.S. Navy that provided an insightful and crucial training support to Pakistan Navy enabling it to conduct operations in long range in the Indian Ocean and the proposal of procuring the submarine was met with favourable views in 1963 due to the prospect of the Soviet Navy leasing a submarine to the Indian Navy. After seeing the U.S. contribution, the United Kingdom decided to provide training and education to Pakistan Navy on submarine operations, and in 1964, PNS Ghazi was commissioned from the United States under the Security Assistance Program (SAP).

Even though, neither the Navy nor the Air Force was notified of the Kashmir incursion in 1965, the Navy was well-prepared at the time when the second war broke out between Pakistan and India in 1965. The naval chief Admiral Afzal Rahman Khan ordered all war units of the Pakistan Navy to take up defensive positions off the coast, but did not order any offensive operations in the Bay of Bengal. As the Indian Air Force's repeated sorties and raids disrupted PAF operations, the Navy assumed a more aggressive role in the conflict. On 2 September, the Navy deployed its first long-range submarine, PNS Ghazi under Commander K. R. Niazi which was charged with gathering intelligence on Indian naval movements that stalked the diverting threats posed by the aircraft carrier INS Vikrant.

On the night of 7/8 September, a naval squadron comprising four destroyers, one frigate, one cruiser, and one submarine, under the command of Commodore S. M. Anwar, launched artillery operation— an attack on the radar facilities used by the Indian Air Force in the small coastal town of Dwarka. The operation ended with limited damage to the area. After gunnery bombardment, Ghazi was deployed against the Indian Navy's Western Naval Command at Bombay on 22 September and ended her operations and reported safely back to Karachi Naval Dockyard on 23 September 1965.

The Pakistan Navy explored the idea of installing Russian missile system on former British frigates but Soviets refrained from doing so due to objections from India.

After the war, the United States imposed an arms embargo on Pakistan and Pakistani military began exploring options for military procurement from China, France, and Soviet Union. The United Kingdom offered the Navy to jointly built the Type 21 frigate but was rejected by Ayub administration that would only allow the financial capital to be spent on submarine procurement.

In 1966, the Pakistan Navy established its own special operations force, the Navy Special Service Group (Navy SSG) after the recommendations from the United States Navy. In 1966–70, Pakistan Navy had been well aware of massive procurement and acquisitions of weapon systems being acquired from the Soviet Union and United Kingdom, and the danger it will posed to Pakistan. In 1966–69, there were series of unsuccessful talks of acquiring the warships from the Soviet Navy which ended with no yielding results. The Soviet Union offered to sell their Osa-class missile boat but Pakistan Navy wanted the Styx missiles to be installed in frigates in a believe that the missile boats were not big enough to meet the Pakistani requirements in operating in the Indian Ocean. The Russians later determined to their strategic interests lay with India and allowed the developing relationship with Pakistan to wither.

Difficulties arose between and after the arms embargo was lifted by the United States which lifted based strictly on cash-and-carry basis. Pleas for strengthening the Navy in East Pakistan were ignored due to monetary issues and financial constraints restricted the Navy's capabilities to function more efficiently. In 1968, the Daphné-class submarines were procured from France while operating Tench-class submarines that was refitted and upgraded by the Turkish Navy. Due to the Egyptian blockade of the Suez Canal, the Navy had to execute a notable submerged circumnavigation operation from the Indian Ocean through the Atlantic Ocean in order to undergo a refit program at the Gölcük Naval Shipyard in Turkey which was the only facility to manage the refitting and mid-life upgrades of military computers of the Tench class. Despite reservations harboring by the Navy NHQ about the ageing Ghazi, she was sailed under the command of Commander Ahmed Tasnim starting from the Karachi coast in Indian Ocean to Cape of Good Hope, South Africa, through the Atlantic Ocean and ended at the east coast of the Sea of Marmara where the Gölcük Naval Shipyard was located.

In 1968–69, the Navy NHQ staff began its tussle with the AHQ staff over the issue establishing the naval aviation who feared the loss of fighter jets and their pilots in the sea and was hostile towards this idea. The United States entered in discussing the transfer of P3B Orion aircraft to the Navy in 1970 with Yahya administration but were not procured until the end of the 1970s. In 1970, the foreign relations between Pakistan and East Pakistan further deteriorated and the Navy knew that it was impossible to defend East Pakistan from approaching Indian Navy. Series of reforms were carried when Navy's serious reservations were considered by the Yahya administration and East Pakistanis were hastily recruited in what was known as Eastern Naval Command (Pakistan) but this proved to be disaster for Navy when majority of Bengali naval officers and ~3,000 sailors defected to India to join the Awami League's military wing– the Mukti Bahini. Such events had jeopardised the operational scope of the Navy and the Navy NHQ staffers and commanders knew very well that it (Navy) was ill-prepared for the war and Pakistan was about to learn the consequences of disconnecting strategy from reality.

By 1971, the Navy NHQ staffers and their commanders knew very well that the Pakistan Navy was poorly represented in East Pakistan (now Bangladesh) and there was no main infrastructure to conduct defensive operation against the Eastern Naval Command of Indian Navy in Bay of Bengal. The Navy was only able conducted the riverine-based operations that was being undertaken by the Pakistan Marines with the assistance from the Navy Special Service Group, code named, Barisal, in April 1971. Although, the Governor of East Pakistan, Vice-Admiral S.M. Ahsan, made efforts to increase the naval presence and significance in 1969 but the Indian Navy's Eastern Naval Command continued to pose a significant threat since it had capability of conduct operations in long-range areas.

Furthermore, the defections from Navy's Bengali officers and sailors had jeopardise the Navy's operational scope who went onto join the Awami League's militant wing, the Mukti Bahini in a program known as Jackpot. Though, the program was disrupted by the Navy from further annihilation but the naval facilities were severely damaged due to this operation on 15 March 1971. East-Pakistan's geography was surrounded by India on all three landward sides by the Indian Army as the Navy was in attempt to prevent India from blocking the coasts.

During this time, the Navy NHQ was housed in Karachi that decided to deploy the newly MLU Ghazi submarine on East while Hangor in West for the intelligence gathering purposes.

At the end of East-Pakistan crisis.... We (Eastern Command) had no intelligence and hence, were both deaf and blind with the Indian Navy and Indian Air Force pounding us day and night....

— Admiral Mohammad Sharif, to U.S. Admiral Zumwalt in 1971

With no naval aviation branch to guard the Karachi port, the Indian Navy breached the seaborne borders of Pakistan and successfully launched the first missile attack, consisting of three Soviet-built Osa-class missile boats escorted by two anti-submarine patrol vessels on 4 December 1971. Nearing Karachi's port area, the Indian Navy's squadron launched Styx missiles anti-ship missiles, which the obsolescent Pakistani warships had no viable defence against. Two of the warships, PNS Muhafiz and PNS Khaibar, were sunk, while PNS Shahjahan was damaged beyond repair. After the attacks, the Indian Navy's missile boat squadron safely returned to its home base without sustaining any damages.

On 8 December 1971, Hangor commanded by its Commander Ahmed Tasnim, sank the Indian frigate INS Khukri off the coast of Gujarat, India— this was the first sinking of a warship by a submarine since World War II, and resulted in the loss of eighteen officers and one-seventy six sailors of the Indian Navy while the inflicting severe damages to another warship, INS Kirpan, by the same submarine. The Pakistan Air Force now covering for Karachi made several of the unsuccessful attempts to engage the Indian Navy's missile boat squadron by carrying out the aerial bombing missions over the Okha Harbor– the forward base of the Indian Navy's missile boat squadron. The Indian Navy retaliated with a second missile attack on Pakistan's coast on the night of 8 December 1971 when a small flotilla of Indian vessels, consisting of a missile boat and two frigates, approached Karachi and launched a missile attack that sank the Panamanian cargo ship Gulf Star, PNS Dacca and the British merchant ship SS Harmattan were damaged.

The missile-based attacks were the complete success for the Indian Navy, and a psychological trauma for Pakistan Navy, the human and material cost severely cutting into its combat capability, nearly 1,700 sailors perished at the barracks.

The commercial pilots from the Pakistan International Airlines volunteered to conduct air surveillance missions with the Pakistan Air Force, but this proved less than helpful when the Pakistan Navy's forward observer team, led by Cdre. A. W. Bhombal misidentified their own larger frigate, PNS Zulfiqar, as an Indian missile boat, giving clearance to the F-86 fighter jets of the Pakistan Air Force which made several attack runs before finally identifying Zulfiqar by the Navy NHQ. This serious friendly fire incident resulted in further loss of navy personnel, as well as the loss of the ship, which was severely damaged and the Pakistan Navy's operational capabilities were now virtually extinct, and morale plummeted. The Indian Navy observers who watched the raid nearby later wrote in their war logs that the "PAF pilots failed to recognize the difference between a large PNS Zulfiqar frigate and a relatively small Osa missile boat." The PAF, however, contested this claim by holding Cdre. Bhombal of the responsibility of misidentifying his own warship and giving clearance to the PAF to mount an attack on their own ship.

The Navy's only long range submarine, Ghazi, was deployed to the area but, according to neutral sources, it sank en route under mysterious circumstances. Pakistani authorities state that it sank either due to internal explosion or detonation of mines which it was laying at the time. The Indian Navy claims to have sunk the submarine.

The submarine's destruction enabled the Indian Navy to enforce a blockade on then East Pakistan. According to the defence magazine, Pakistan Defence Journal, the attack on Karachi, Dhaka, Chittagong and the loss of Ghazi, the Navy no longer was able to match the threat of Indian Navy as it was already outclassed by the Indian Navy after the 1965 war.

The damage inflicted by the Indian Navy and Indian Air Force on the Navy stood at seven gunboats, one minesweeper, two destroyers, three patrol craft, eighteen cargo, supply and communication vessels, and large-scale damage inflicted on the naval base and docks in the coastal town of Karachi. Three merchant navy ships; Anwar Baksh, Pasni and Madhumathi; and ten smaller vessels were captured. Around 1,900 personnel were lost, while 1413 servicemen (mostly officers) were captured by Indian forces in Dhaka. The Indian Navy lost 18 officers and 176 sailors and a frigate, while another frigate was damaged and a Breguet Alizé naval aircraft was shot down by the Pakistan Air Force.

According to one Pakistan scholar, Tariq Ali, the Pakistan Navy lost half its force in the war. Despite the limited resources and manpower, the Navy performed its task diligently by providing support to inter-services (air force and army) until the end.

According to the testimony provided by the Admiral Mohammad Shariff in 2015, the primary reason for this loss has been attributed to the High Command's failure in defining a role for the Navy, or even considering Navy as military in general. Since then the Navy has sought to improve the structure and fleet by putting special emphasis on sub-surface warfare capability as it allows for the most efficient way to deny the control of Pakistani sea lanes to an adversary. In a thesis written by Dr. P. I. Cheema in 2002, Ayub Khan, who had enjoyed considerable influence on Pakistan's national politicians, did not fully understood the Navy as a military service or neither comprehend the importance of safeguarding the sea lines of communication, which prevented the development of the Navy as a potent force as it should have in the 1970s.

After 1971 war, steps were taken to modernise and increase the operational scope of the Navy. Unlike the army or the air force, the naval officers were able to continue their military service with the Navy, and their promotions were relatively quicker than other military branches in 1972–74.

In January 1972, the Bhutto administration formed the POW Commission to investigate the number of war prisoners held by the Indian Army in East and submitted the request to the Supreme Court of Pakistan to investigate the causes of the war failure with India in 1971. After concluding a quick visit in the United States in 1972, President Bhutto used his administrative powers to dishonorably discharge the commission of five senior admirals in the Navy, appointing the junior most H. H. Ahmed as the first Chief of Naval Staff of the Navy. In 1973, the Navy NHQ was permanently moved to Islamabad to provide synergy with the Army GHQ in Rawalpindi.

In 1974, the Naval Aviation branch was established with the transfer of the Westland Sea King helicopters from the United Kingdom in 1975, followed by test firing the surface-to-ship Exocet missile as a befitting response to the Indian Navy in 1979. With the ability to fire the land-based Exocet missile from a reconnaissance aircraft, the Navy became the first of its kind in the South Asia to acquire land-based ballistics missile capable long range reconnaissance aircraft.

In 1976, the Navy moved towards successfully acquiring the military computers from the British firm, the Ferranti, to increase its defence's for its coastlines. The War Enquiry Commission noted the lack of strategic communication and the grand strategy between the four-branches of the military during the conflict and wars with India, recommending the establishment of the Joint Chiefs of Staff Committee to maintain strategic military communication between the inter-services and the federal government, that is to be chaired by the appointed Chairman joint chiefs as the government's principal military adviser. In 1976, Navy saw its first four-star rank admiral when Mohammad Shariff was promoted to this rank, and later becoming the first admiral to be appointed as the Chairman of Joint Chiefs Committee in 1977. In 1977, the United States reportedly transferred the two refitted Gearing-class destroyer to the Pakistan Navy, which were much superior to the British frigates, followed by obtaining more destroyers from the U.S. Navy in 1982–83.

During this time, the Navy to diversify its procurement with defence deals made with China, France, and the United Kingdom but the dependence grew on China when the Navy acquired the anti-submarine warships that gave the Navy credible sea-denial capability. In 1979, the France offered to sell their Agosta-70A-class submarine and was immediately acquired which were commissioned as Hurmat and Hashmat. Induction of the Agosta-70A class gave Pakistan Navy a depth advantage over the Indian Navy, and gave the Navy an ability to conduct operations in deeper Indian Ocean at wider range.

In 1982, the Reagan administration submitted the proposal of US$3.2 billion aid for Pakistan that was aimed towards economic uplift and security assistance to the United States Congress as the Navy entered in successful negotiation of obtaining the Harpoon system, despite the strong Indian lobby opposing and objecting of this deal. In 1985, the Navy bought the Mirage 5V aircraft for the naval role and were equipped with the Exocet A39 missile that gives the capability of sea denial to the Pakistan Navy. With the induction of the missile systems, long-range and depth endurance submarines, missiles destroyers, fighter aircraft, and establishment of the Pakistan Maritime Security Agency, the Pakistan Navy eventually ended the Indian Navy's control over the Indian Ocean, and the Indian Navy's confidence that it could contain the Pakistan Navy at shorelines.

Eventually, the Pakistan Navy began its wartime deployment in Middle Eastern countries through the Persian Gulf and deployed its war assets in Saudi Arabia in support of the U.S. Navy's fleet in wake of the events involving the Iran–Iraq War and tensions with Libya. In 1982, the Reagan administration approved US$3.2 billion military and economic aid to Pakistan with Pakistan acquiring eight Brooke and Garcia-class frigates from the United States Navy on a five-year lease in 1988. A depot for repairs, USS Hector followed the lease of these ships in April 1989. This was done due to the Zia administration's co-operation with the Reagan administration against the Soviet Union's invasion in Afghanistan.

After the Russian troops withdrawal from Afghanistan in 1989, the Bush administration imposed the arms embargo on Pakistan by uncovering the existence of the covert atomic bomb program to the United States Congress, which ultimately refrained the transfer of the maritime patrol aircraft, missile systems, and defence software on 1 October 1990. With the expiration of the lease of the Garcia and Brooke-class guided missile frigates, the Navy had to return the frigates to the United States that were sold to India for scrapped metals, and Navy to faced the problems for adequate funding towards the modern Navy. The embargo seriously impaired the Navy's operational scope and paralysed its ability to operate in the Indian Ocean, since the Navy's fleet was composed of entirely the former U.S.-built warships.

Since 1987, the Pakistan Navy had been interested in acquiring the Type 21 frigates from the United Kingdom, and the Navy turned to the Royal Navy for an immediate purchase which was approved in 1993 whose expensive refitting and technological upgrades had to carried out by Pakistan itself at their Naval Base in Karachi over the years. In 1994, the Pakistan Navy entered in lengthy, complicated, and controversial negotiation with France to acquire the long-range submarine technology by dismissing the idea of procuring nuclear-powered submarine from China due to noise issue that the Indian Navy was quiet able to track. Despite embargo, the United States Navy maintained its relations with Pakistan Navy, inviting the Pakistanis to participate in the Inspired Siren in 1994, and gave the Pakistan Navy instructions and run down on the nuclear submarine and aircraft carrier operations. In an attempt to warm the political relations with the United States, the Pakistani military joined the U.S. actions in the Somali Civil War, conducting wartime patrol in the Somali coast.

In 1994, the Navy was deployed in support of the U.S. Navy and extended its support in 1995 to participate in Operation United Shield to conclude its side of operation after evacuating personnel and equipment of the army, marines, and air force. By 1996, the Brown amendment was introduced that allowed the uplifting of the embargo on Pakistan, allowing the transfer of the maritime patrol aircraft to the Navy.

By 1997, the controversy over the technology transfer from France had tarnished the public image of the Navy with the arrest of naval chief when several cases were levelled on political and military leadership of the Navy. Despite India's strong objections in France, the air-independent propulsion was transferred to Pakistan which built the Agosta 90B-class submarine, capable to operating in Indian Ocean and at higher submarine depth. In 1999, the Navy saw the public disagreement with the federal government over the issue of Pakistan Army's engagement with Indian Army in Kashmir and over the rightful appointment of the Admiral Fasih Bokhari as Chairman joint chiefs. Pakistan Navy was forced to deploy its existing war assets when the Indian Navy deployed its warships near Korangi Creek Cantonment and Port of Karachi with their codename: Operation Talwar.

On 10 August 1999, a serious incident took place in Sir Creek region when the Indian Air Force shot down the Naval Aviation aircraft that resulted in deaths of 16 naval personnel, mostly officers. On 29 August 1999, another aircraft of the Navy, P3C Orion, was lost due to an accident with the loss of twenty one lives.

Over the issue of the Indian Air Force's shot down of the aircraft, the Navy filed a lawsuit against the Indian Air Force at the International Court of Justice, but the claim was later dismissed due to over-reaching of the court's mandate.

Pakistan fully endorse the requirements of a strong navy, capable of safeguarding Pakistan's sea frontiers and her Lines of Communication, monitoring and protecting her exclusive economic zone. Continuous efforts are at hand to provide the best available equipment to the Navy despite all economic constraints.

— Pervez Musharraf, 1999

After his incident in 1999, another proposal was raised to switched the air-independent propulsion of Agosta submarine to substitute with nuclear propulsion, however the proposal was dismissed.

After the 9/11 terrorist attacks in the United States, the sanctions on Pakistan were eventually uplifted, allowing the Navy to procure the U.S.-built weapon systems and warships to regain its ability to operate in the Indian Ocean as it became involved in war preparations during the standoff with India in 2001–02. In 2001, the Navy took serious consideration of deploying the nuclear weapons on its submarines although none of the nuclear weapons were ever deployed in the submarines.

In 2003–04, there were several proposals made for acquiring the vintage aircraft carriers but the Navy itself had dismissed the idea since the country has not aspired to have an aircraft capability. In 2002–03, the Pakistan Navy deployment took place in the Indian Ocean, participating in the naval drills to combat terrorism from seaborne platforms, and eventually entered in defence negotiations with China for acquiring the technology to designing and building the guided missile frigates— the F-22P guided missile frigates were eventually built it in 2006–15.

Since 2004, the Navy's deployment took place in Indian Ocean, playing a crucial role in the multinational NAVCENT in Bahrain, and took the leadership of the CTF-150 and CTF-151 as well as taking active participation in the Operation Enduring Freedom in 2006–10. In 2008, the task force group consisting of PNS Badr, PNS Shah Jahan, PNS Nasr, and the Pakistan Air Force's Explosive Ordnance Disposal participated in the Exercise Inspired Union with the U.S. Navy in the Indian Ocean to develop skills in a prevention of seaborne terrorism.

Its deployment in the War on terror also included their actions in the War in Afghanistan when the Navy's special forces were deployed to take participation in the Operations: Black Thunderstorm, Rah-i-Nijat, Mehran, and the Help.

Despite its seaborne mission, the Navy had played an active role in controlling the insurgency in former tribal belt in Western Pakistan, mostly taking roles in managing logistics and intelligence gathering as well as conducting ground operations with the army in Western areas to track down the al-Qaeda operatives. From 2010 to 2011, the Navy was in a brief direct conflict with the violent TTP group and al-Qaeda, and its Naval Intelligence was able to track down the infiltrated militants within the ranks of the Navy.

In 2015, the Navy was deployed in support of the Saudi-led blockade of Yemen after accepting the request from the Saudi Arabia. As of current, the Navy continues increase its operational scope in the Indian Ocean and reportedly successfully entering in defence talks with Turkey to jointly built the MILGEM project in Pakistan in 2018–2019 while it had earlier announced to start the building the program of the nuclear submarine for its current operational capabilities in 2013.

Leadership in the Navy is provided by the Minister of Defense, leading and controlling the direction of the department of navy from the Naval Secretariat-II at the Ministry of Defense, with the Defense Secretary who is responsible for the bureaucratic affairs of the army's department. The Constitution sets the role of the elected President of Pakistan as the civilian Commander-in-Chief of the Pakistan Armed Forces while the Prime Minister of Pakistan served as the Chief Executive of the Pakistan Armed Forces, both the people-elected civilians, the President and Prime minister, maintains a civilian control of the military.

The Chief of Naval Staff (CNS), an appointed four-star rank admiral, is a principal military adviser on the naval/maritime security affairs to the Federal government and is a senior member of the Joint Chiefs of Staff Committee (JCSC)— a military body that advises and briefs the elected civilian Prime Minister and its executive cabinet on national security affairs and operational military matters under the Chairman of the Joint Chiefs of Staff Committee.

The war functions of the Navy is controlled from the single combat headquarters, the Navy NHQ, located in Islamabad at vicinity of the Joint Staff Headquarters and the Army GHQ in Rawalpindi Cantonment in Punjab in Pakistan. The Chief of Naval Staff controls and commands the Navy at all levels of operational command, and is assisted by number of Principal Staff Officers (PSOs) (Staff Commanders) who are commissioned at the three-star rank and two-star rank admirals. The Staff Appointments marked in the light goldish yellow color are the most important seats at NHQ which play a very important administrative role for the proper functioning of the Pakistan Navy and its assets.

Due to the influence from the Royal Navy and later by the United States Navy since its earliest inception, the Pakistan Navy has a unique command structure and the navy's functionality is divided in various branches.

There are seven military staff commands in the navy that are in fact administrative, directed by the several appointed Deputy Chief of the Naval Staff (DCNS) and often assisted by the Assistant Chief of the Naval Staff (ACNS) holding the rank of commodore a one-star rank senior officer reporting directly to their respective Deputy Chief of the Naval Staff (DCNS). The Deputy Chiefs Of Naval Staff are usually holding either the two-star or three-star ranks.The each and appointed Deputy Chief of the Naval Staff head or commander of their respected branch reports directly to the Chief of the Naval Staff (CNS) at Navy NHQ in Islamabad of their respected command.

The military administration of the Navy under the Naval Chief based in the Navy NHQ includes its Principal Staff Commands and Principal Staff Officers:

Principal Staff Commands at NHQ	Call sign	Principal Staff Officers	Notes
Vice Chief of the Naval Staff	VCNS	Vice Admiral Ovais Ahmed Bilgrami HI(M), Ops	The Second in Command of The Pakistan Navy.
Deputy Chief of the Naval Staff (Operations)	DCNS-O	Vice Admiral Raja Rab Nawaz, HI(M), Ops	Head of Operations Branch and Organization in the Pakistan Navy.
Deputy Chief of the Naval Staff (Materials)	DCNS-M	Vice Admiral Abid Hameed, HI(M), Engg	Head of Materials Branch and Organization in the Pakistan Navy.
Deputy Chief of the Naval Staff (Supply)	DCNS-S	Rear Admiral Syed Ahmed Salman, HI(M), Supp	Head of Supplies Branch and Organization in the Pakistan Navy.
Deputy Chief of the Naval Staff (Projects)	DCNS-P	Rear Admiral Shafquat Hussain Akhtar SI(M),Ops	Head of Projects Branch and Organization in the Pakistan Navy.
Deputy Chief of the Naval Staff (Trainning and Personnel)	DCNS-T&P	Rear Admiral Muhammad Saleem HI(M),Ops	Head of Training and Personnel Branch and Organization in the Pakistan Navy.
Deputy Chief of the Naval Staff (Administration)	DCNS-A	Rear Admiral Syed Ahmed Salman, HI(M), Supp	Head of Administrations Branch and Organization in the Pakistan Navy.
Deputy Chief of the Naval Staff (Welfare and Housing)	DCNS-W&H	Rear Admiral Shifaat Ali Khan, HI(M), Ops	Head of Welfares and Housings Branch and Organization in the Pakistan Navy.

The Organizations and the Heads of Services operating in the Pakistan Navy and reporting directly to the Naval Chief are as follows:

Organizations	Call sign	Heads of Services
Director General, Naval Research and Development Institute	DG NRDI	Rear Admiral Hussain Sial, HI(M), Engg
Director General, Command, Control, Communication, Computers and Intelligence	DG C4I	Rear Admiral Jawad Ahmed, HI(M), Ops
Naval Secretariat, Naval Secretary	NS	Rear Admiral Imtiaz Ali, HI(M) TBT & Bar, Ops
Director General, Naval Intelligence	DG NI	Rear Admiral Shahzad Hamid, SI(M) TBT, Ops
Director General, Public Relations	DG PR	Commodore Ahmed Hussain, SI(M), Ops

Each branch in the navy offers specialisation and officers interested in joining the particular service have to pass aptitude tests before attending the specialised school that usually last for two to three years, in which the officer is able to attain a college degree.

Military administration in the Navy

administrative branches in the Navy	call sign	specialization and qualification badges		administrative branches in the Navy	call sign	specialization and qualification badges
Naval Operations	Ops	Surface warfare Underwater warfare Electronic Warfare Communication Navigation NBCD		Naval Supplies	S	Supply Badge
Logistics	Log	Logistics Badge		Mechanical	Mech	Ship Mechanical Engineering Badge
Judge Advocate General Corps	JAG	JAG Badge		Education	Ed	Education Badge
Weapons Engineering Branch	WEB	WEB Badge		Marine Engineering Branch	MEB
Aviation	AVN	Naval aviator badge		Music	MUS	Music Badge
Medical	MED	Medical Badge		Naval Police	NP	Naval Police Badge
Naval Intelligence	NI	Navy Intelligence Badge		Marines Corps	MC	Marines Badge
Navy SEALs	SSGN	SSGN Badge		Maritime Security Agency	MSA	MSA Badge
Special Branch	SB	IT Badge		Chaplain (Khatib) Service	CS

Since its restructuring and reorganisation over the several years, the Pakistan Navy now operates eight operational and tactical field commands and also two major type commands, two of the important commands of aviation and submarines are reporting directly to the senior Pakistan Fleet Command. Each command is headed by a senior flag officer who usually holds a ranks of three-star rank: Vice-Admiral and two-star rank: Rear-Admiral. The appointment to the senior fleet commander known as s Commander, Pakistan Fleet leads the navy's entire fleet with a responsibility of deploying the entire combat formations of the navy.

Geographically, there are three administrative commanders, such as Commander Karachi (COMKAR), Commander Central Punjab (COMCEP), and Commander Northern (COMNOR), who administer the bulk of naval installations, offshore establishments, and training facilities besides the seven oceanic based commands.

In 2012, the Pakistan Navy established the Naval Strategic Forces Command that has area responsibility of exercising the deployment of sea-borne nuclear weapons and is described by the military as the "custodian of the nation's nuclear second strike capability."

The peacetime commands and the Commands in the Navy allocated are given below.

Operational Commands in the Pakistan Navy

Headquarters	Navy NHQ, Islamabad in Pakistan
Operational, Tactical and Type Commands	Call sign	Commander	Subordinate combat squadrons and arms	Notes
Commander, Pakistan Fleet	COMPAK	Rear Admiral Abdul Munib, SI(M), Ops	Subordinate squadrons 25th Destroyer Squadron 18th Destroyer Squadron 9th Auxiliary Squadron 21st Auxiliary Squadron 10th Patrol Squadron Fast Patrol Squadron Commander Naval Aviation- COMNAV Commander Submarines- COMSUBS	The war-fighting command responsible for operational deployments of the Surface, Submarine, and Aviation Commands to ensure the operational readiness and assurances of the Navy.
Commander, Karachi	COMKAR	Vice Admiral Muhammad Faisal Abbasi, HI(M), Ops	Subordinate offshore establishments PNS Bahadur– Submarine school PNS Himalaya– Boot camp PNS Karsaz PNS Rahat Pakistan Naval Academy PNS Rahnuma – HR Department PNS Shifa School of Logistics and Management PNS Nigraan – Naval Police HQ	Directs the offshore establishments, training schools, military protocol, and ensuring coastal defence of Karachi coast.
Commander, Coast	COMCOAST	Rear Admiral Faisal Amin, SI(M), Ops	Subordinate branches COS Marines Corps Naval Observatory PNS Iqbal PNS Qasim Marines Base Sir Creek Manora Base Pakistan Naval Air Defense	Directs the coastal command by ensuring the coastal defences of Pakistan from Iranian border in West to Indian borders in East.
Commander, Naval Strategic Forces Command	CDR NSFC	Vice Admiral Abdul Samad, HI(M), Ops	Subordinate commands Navy Special Service Group Deployment of seaborne-nuclear weapons	This command was identified by the military as Custodian of nuclear second strike capability
Commander, Logistics	COMLOG	Rear Admiral Muhammad Sohail Arshad, HI(M), Engg	Subordinate commands Naval Dockyard Weapons Depot PNS Dilawar– Logistics Base Commander Depot– COMDEP	Directs the logistics command to oversee the maintenance, military logistics and material readiness for construction warships at the shipyard.
Flag Officer, Sea Training	FOST	Rear Admiral Khyber Zaman, HI(M), Ops		This Command oversees the training deployment of the Pakistan Navy Fleet
Commander, Central Punjab	COMCEP	Rear Admiral Azhar Mahmood, SI(M), Ops		Oversees the deployments of Marine detachment and operations of the War College in Punjab
Commander, West	COMWEST	Rear Admiral Adnan Majeed, SI(M), Ops		Directs the Navy's combat units in the Western Pakistan. Subordinate commands Pakistan Naval War College– Lahore PNS Punjab
Commander, North	COMNOR	Commodore Saqib Ilyas SI(M), Ops -		Directs the Navy's combat units in Northern Pakistan and reports to Principal Staff Commands at NHQ.
Commander, Depot	COMDEP	Commodore Fareed Amin SI(M), Supp		Directs the Naval Depots Command to oversee all the naval supplies and materials being stored and distributed in the Pakistan Navy and reporting directly to COMLOG
Commander, Naval Aviation	COMNAV	Commodore Syed Talat Hussain, SI(M), Ops		Directs the Naval Aviation Command but reporting directly to COMPAK
Commander, Submarines	COMSUBS	Commodore Mazhar Bashir, SI(M), Ops		Directs the Submarine Command but reporting directly to COMPAK
Director of Procurement, Navy	DP NAVY	Commodore Muhammad Shahnawaz Khan, SI(M), Supp -		This Command deals in the purchasing of certain military equipments and supplies for the navy and reports to DCNS-S

The Special Service Group (Navy) (SSG(N)), colloquially known as the SSGN is an elite unit that conducts unconventional warfare, combat diving, naval interdiction, and asymmetric warfare operations, established under the guidance of the United States Navy's SEALs in 1966.

The Navy Special Service Group is headquartered at PNS Iqbal in Karachi where the physical conditioning and weapon tactics training take place. The Navy Special Service Group's specialisation further includes training and mastery in the visit, board, search, and seizure methods, naval interdiction, and security operations to prevent seaborne-based terrorism.

The Navy Special Service Group is a tighter unit composed of highly qualified and selected personnel who are modelled on and inspired by the U.S. Navy SEALs training and tradition. The actual number of personnel of Navy Special Service Group is classified and their deployment are also subjected to classified information.

In 1970–71, the Navy established the Pakistan Marines to support the amphibious warfare operations and were initially influenced by the United States Marines Corps but the Marines component was decommissioned by the federal government in 1974. On 14 April 1990, the Pakistan Marines were again recommissioned in the Navy with about 2,000 personnel. The advanced training of the Marines are often takes place with the Pakistan Army at their School of Infantry and Tactics in Quetta in Balochistan.

The 1st Marines Battalion, the special operation unit, of the Pakistan Marines is specifically trained by the Pakistan Army to conduct infiltration and anti-aircraft warfare operations. The 1st Battalion is currently deployed in Sir Creek.

The military doctrine and philosophy of the Pakistan Navy is primarily directed towards preventing the Indian Navy repeating the 1971 blockade of the Pakistani coasts. From 1947 until 1971, the Pakistan Navy was effectively little more than a coast guard because the Government of Pakistan did not give importance to the strategy of protecting the sea lines of communication. In 1971, the Indian Navy ultimately played a decisive role by enforcing a blockade of Chittagong and Karachi, the only maritime outlets of East Pakistan and West Pakistan respectively. The Navy was unable to break the blockade leading to Pakistan's economic and military resources being severely drained and communication was limited between the two wings of the country. Subsequently, the federal government increased the funding of the Navy.

Since 1971 the Navy tactical doctrine has included the acquisition, development, employment, and aggressive deployment of the long-range and depth reaching submarines in an effort to target and destroy its adversaries by attacking surface warships before reaching the country's ports. The mining of the Karachi's harbour is also taken as a serious consideration of preventing the enemy from launching the missile attacks in the port city of Karachi.

In 1983–85, the Navy commissioned the Dassault Mirage 5 from France whose weapon system included the naval variant of the Exocet missiles and are aimed towards engaging the Indian Navy's aircraft out to 500 kilometres (310 mi) in the Indian Ocean.

The routine deployment of the surface fleet as part of the Combined Task Forces provides the opportunity to the safeguard the sealines of communications. Since 1999, the Pakistan Marines's special reconnaissance forces has been deployed in the Sir Creek region are aimed towards offshore protection against the incursions from the Indian Army's Para Commandos from the sea while taking the initiatives of deployment of the special forces groups behind the enemy lines through insertion by the HALO/HAHO airdrop or by using the midget submarines.

Responding to the development of the INS Arihant, the Pakistan Navy reportedly announced the launch of the nuclear powered submarine program to counter the submarine threat in 2012.

The Navy eventually pushed for attaining the naval-based nuclear second-strike capability in 2017 when the ISPR announced the Pakistan Navy's to have attained the sea-based second strike capability when it launched the nuclear SLCM based on the Babur cruise missile, though the range of the SLCM remains to be at the short range.