The Point Nepean Quarantine Station is a former quarantine and military training facility in Portsea, Victoria, Australia on the Mornington Peninsula. It was established as a quarantine in 1852 following the Ticonderoga's arrival at the heads of Port Philip with a significant number of passengers with scarlet fever. It ceased operation as a quarantine in 1980, but was used by the military for training purposes since the 1950s (see Officer Cadet School). Currently, it hosts markets and similar events amongst the flat area and is part of the Point Nepean National Park. There is a shuttle bus to Fort Nepean that terminates at the Quarantine, as well as rentable bicycles to ride around the park. It is managed by Parks Victoria.

A quarantine was established at Sydney's North Head in 1832 to preserve the colony's lack of European diseases, specifically cholera. New South Walesquarantine laws were carried over into Victorian law after separation. The Port Phillip District (Victoria) set up a quarantine at Point Ormond, and later Hobsons Bay, in the 1840s. Immigration to Victoria increased when gold was found in the north-west, and the requirement for a proper quarantine became more important.

Point Nepean was selected as the site for a new quarantine, and the state government assigned £5000 for a 'sanatorium'. The site was leased by Patrick Sullivan, the son of a settler, and William Cannon, both of whom were involved in lime burning. The site already had several buildings built by Sullivan and Cannon, including a stone house, three wattle and daub structures, a dairy and a lime kiln each. In October 1812, Governor La Trobe and General Surveyor Robert Hoddle found that their leases ended that year, and instructed their leases not be renewed for the next year.

In November, less than a month later, the Ticonderoga sailed through the heads with almost three hundred people onboard with scarlet fever and typhus, and a further hundred dead. The ship was from Liverpool, leaving with 714 passengers and 48 crew. The news reached Melbourne within a day via Captain Wylie of the Champion, who has passed the Ticonderoga at the heads. Captain Charles Ferguson investigated and came back to Governor La Trobe on November 9th, reporting that Sullivan had been moved from the site and the passengers of the Ticonderoga had set up tents on the shore.

Sullivan and Cannon's buildings were used to house the sick, beginning the quarantine. Ferguson found that many of the passengers happened to be stonemasons, and instructed them to build a storage building on the site, and suggested to La Trobe that a building be built for the healthy inhabitants of the quarantine. It was officially referred to as the "Sanitary Station", until the 1880s, when "Quarantine Station" became more commonly used.

Between 1852 and 1887, several buildings were proposed, half constructed, and then left unfinished because of a lack of timber. This also saw many people buried without coffins. The hospital could house fifty patients, (and a further 450 in tents) which quickly became inadequate. Dr James Reed, resident doctor was denied an extension of the hospital by the government, as they wanted to build out the station through purpose and planning, as opposed to its rapid growth due to the Ticonderoga's emergency.

Between 1888 and 1889, five limestone buildings were constructed, which are still there today. Two were built on a hill as hospitals for the sick, while three were built in a line on the flat land to house healthy passengers. A pier and cookhouse were also constructed at this time. Soon after, the Tudor arrived with almost everyone onboard sick. This tested the new buildings' capacity, but also brought a new issue. To prevent illness being spread through possessions, luggage and clothes were treated in boiling water, which upset the passengers, as much of their belongings had been ruined and their clothes shrunk. Dr Reed wrote in his report that a more effective, less destructive method of sanitation would be through an oven-like machine, but this would only be implemented 40 years later.

Into the 1860s, there was a downturn in immigration as the gold rush subsided, also leading to a decrease in the colony's income. This, partnered with better hygiene on ships, cast doubt on the usefulness of the Sanitary Station and stalled construction of any new buildings – including the oven-like machine suggested by many doctors from the quarantine. The government conducted an inquiry into the quarantine and found the conditions unsuitable. They considered relocation of the quarantine and repurposing the Portsea site for a mental asylum. The staff and Chief Medical Officer fought against this, but the resident doctor was cut, making the staff numbers go from three men to two. This meant the ship's surgeon would have to tend to the patients, once they reached shore, as there was no doctor. Toilets were added to the hospitals.

In 1870, the limestone buildings' uses were switched, so that the hill was used for first and second class, hospitals 3 and 4 on the flats were for steerage class, and the fifth was for isolated, sick patients. It was fenced off in 1890. Telegraph communications were implemented in 1874.

Forty years after it was first suggested, Reed's disinfecting system was built in the early 1900s. A tramway was constructed to take luggage from the pier, into a sanitation chamber where they are heated, and out the other side. In this complex was also a bath house. At federation, the quarantine was transferred to the commonwealth government. A waiting room for healthy patients reboarding the ship was built in 1911, and the following year a weatherboard extension was added to Hospital 5, to house more sick patients.

1916 brought several new buildings to the quarantine. A dining hall for first and second class was built on the hill, connecting to hospitals one and two. An administration building was constructed, including a post office and quarters for police and visiting staff. Stables were also built, using materials from a stable at Police Point (slightly closer to Portsea) and some sheds nearby.

The 1918–1920 flu pandemic pandemic brought new use for the quarantine, and as such, several wooden "influenza huts" were hurriedly built for the influx of patients. These 12 huts, built over five weeks, processed 300 ships between 1918 and 1919 – returning World War One soldiers.

The last notable construction as a quarantine was the addition of a morgue to Hospital five in 1921.

The Point Nepean Quarantine Station continued use into the second world war. In 1952, most of it was turned into the Officer Cadet School. It ceased to operate as a quarantine in 1980, but the Cadet School, School of Army Health and other military uses persisted into the late 1990, as well as housing Kosovar Refugees from the wars in the Balkans.

It was declared part of the Point Nepean National Park in 2009, which now encompasses Police Point, Fort Nepean and Cheviot Beach, the site of Harold Holt's disappearance.

The site today is host to several community markets and shows, as well as being part of Point Nepean National Park, and has a private provider of bicycles and cycling equipment for visitors to ride around the park. On market days, parking is provided on Jarman Oval, adjacent to Quarantine, but on non-event days, there is a permanent asphalt car park in the south, accessed off the one-way loop road system formed by Danson Drive, Defence Road and Ochiltree Road. Immediately to the east of the carpark is the stables, and behind some trees to the west are the influenza huts.

Upon entry from Jarman oval, one will find the isolation hospital and morgue, just north of the influenza huts. East of the isolation hospital are the three flat-land hospitals, Hospital 5, Hospital 4 and Hospital 3. Across Bogle Road from Hospital 3 is the 1900 red brick sanitation buildings, which are often open for the public to look inside. Toward the shore are the waiting room and the pier's remnants. This is the extent of the market grounds.

Further east is the Parade Ground and flagpole, used during the sites' military occupation for marching, although the green existed while it was still a quarantine. Across the parade ground is the administration building, which is the Point Nepean Information Centre and where the bicycle service is run from. Next to the admin building is Badcoe Hall, named after the Victoria Cross winner Peter Badcoe, who attended the Officer Cadet School. This was built in the 1960s by the Cadet school as a gymnasium.

Up the hill is Shepherd's Hut, which predates the quarantine, built by the previous occupants. Two dilapidated 1960s buildings were built on the hill as accommodation for cadets. These are in significant disrepair today. Beyond these lie the remaining two 1850s hospitals (H1 and H2), used for first and second class passengers. Attached to the hospitals is the dining hall, which was built in 1916 and split into two sections (for first and second class) with one kitchen between them. In the 1960s, the building was renovated and used as a mess hall, but are now closed due to asbestos concerns.

The eastmost buildings in the quarantine are the Medical Superintendent's quarters and Chief Officer's cottage. The former was built in 1899 for J Couper Johnston. This portion of the quarantine remained a quarantine while the army was using the rest of the site. The house was used to isolate pregnant women during this period. The Chief Officer's cottage has temporary fence around it and is significantly smaller than the house across the path from it.