In specific cases there were incidents of friendly fire in the Israel–Hamas war. The vast majority of casualties in the conflict were killed by the opposing side, i.e. Israelis killed by Palestinian militants and Palestinians killed by the Israeli military. According to the Israel Defense Forces (IDF), as of May 2024, 49 of the 278 Israeli soldiers killed during the Israeli invasion of the Gaza Strip were killed by friendly fire and in other accidents.

Friendly fire incidents were seen before the Gaza invasion and the 7 October attacks, with a non-commissioned officer shot and killed by IDF troops in Summer 2023 while securing an alley way in Jenin with the elite Egoz commando unit. Two others were killed in the same unit in January 2022 in the Jordan Valley, with both incidents being highlighted as mistaken identities.

After the 7 October attacks Israel mobilized about 360,000 reservists in the IDF, which were to add to their about 169,500 active duty personnel. By January 2024 about 295,000 reservists had reported for duty and many were potentially under trained due to timing concerns before being sent to fight. The IDF has an annual budget of about US$23.6 billion for 2023, and possess a range of highly sophisticated defensive and offensive weaponry.

On 5 December 2023, Israeli hostages released by Hamas met with prime minister Benjamin Netanyahu's war cabinet and claimed that, during the October 7th Hamas-led attack on Israel they were deliberately attacked by Israeli helicopters on their way into Gaza, and were shelled constantly by the Israeli military while they were there. The Israeli broadcaster Channel 12 reported on 16 December that IDF forces had fired on a tractor carrying hostages to Gaza. On 18 December the IDF admitted that "casualties fell as a result of friendly fire on 7 October", but added that "beyond the operational investigations of the events, it would not be morally sound to investigate these incidents due to the immense and complex quantity of them that took place in the kibbutzim and southern Israeli communities due to the challenging situations the soldiers were in at the time."

In January 2024, an investigation by Israeli newspaper Yedioth Ahronoth concluded that the IDF had in practice applied the Hannibal Directive from noon of 7 October, ordering all combat units to stop "at all costs" any attempt by Hamas militants to return to Gaza with hostages. IDF helicopters fired on cars trying to cross into Gaza. It is unclear how many hostages were killed by friendly fire as a result of the order. According to Yedioth Ahronoth, Israeli soldiers inspected around 70 vehicles on the roads leading to Gaza that had been hit by a helicopter, tank or UAV, killing all occupants in at least some cases.

In an interview with Israel's Haaretz, Lieutenant Colonel Nof Erez stated that IDF forces were mostly wiped out on the ground along the Gaza border. This reportedly meant that there was no one that helicopter or drone pilots could communicate with, making the identification of persons on the ground very difficult. According to Erez, "the Hannibal [Protocol], for which we have been conducting drills over the past 20 years, relates to the case a single vehicle containing hostages: you know which part of the fence it comes through, what side of the road it would move to and even which road... What we saw here was a 'mass Hannibal'. There were many openings in the fence. Thousands of people in many different vehicles, both with hostages and without hostages."

A report by a UN Commission published in June 2024 found that the Israel Security Forces applied the Hannibal Directive in several locations, likely killing at least 14 Israeli civilians on 7 October 2023.

A July 2024 Haaretz investigation revealed that the IDF ordered the Hannibal Directive to be used, adding: "Haaretz does not know whether or how many civilians and soldiers were hit due to these procedures, but the cumulative data indicates that many of the kidnapped people were at risk, exposed to Israeli gunfire, even if they were not the target." One of these decisions was made at 7:18 A.M., when an observation post reported someone had been kidnapped at the Erez crossing, close to the IDF's liaison office. "Hannibal at Erez" came the command from divisional headquarters, "dispatch a Zik." The Zik is an unmanned assault drone, and the meaning of this command was clear, Haaretz reported.

A source in the Southern Command of the IDF told Haaretz: "Everyone knew by then that such vehicles could be carrying kidnapped civilians or soldiers...There was no case in which a vehicle carrying kidnapped people was knowingly attacked, but you couldn't really know if there were any such people in a vehicle. I can't say there was a clear instruction, but everyone knew what it meant to not let any vehicles return to Gaza." The same source stated that on 2:00 P.M. a new instruction was given that "was meant to turn the area around the border fence into a killing zone, closing it off toward the west."

Haaretz further reported that at at 6:40 P.M. military intelligence believed militants were intending to flee back to Gaza in an organized manner from near Kibbutz Be'eri, Kfar Azza and Kissufim. In response the army launched artillery at the border fence area, very close to some of these communities. Shells were also fired at the Erez border crossing shortly thereafter. The IDF says it is not aware of any civilians being hurt in these bombardments.

Haaretz notes one case in which it is known that civilians were hit, which took place in the house of Pessi Cohen at Kibbutz Be'eri. 14 hostages were in the house as the IDF attacked it, with 13 of them killed.

In the Hamas led attack on 7 October, around 40 Hamas militants attacked the Be'eri kibbutz in southern Israel and took many Israelis as hostages. At one point, a Palestinian commander asked an Israeli woman, Yasmine Porat, to call the Israeli police as he wanted to negotiate safe passage back to Gaza in exchange for keeping the hostages alive. The Israeli police arrived and engaged in a gun battle with the militants; the militants used the hostages to prevent the Israeli police from killing them. A tank then arrived and fired on the house full of the hostages. Porat said most of the hostages were still alive before the tank arrived. Brig. Gen. Barak Hiram admitted he had ordered the tank to fire at the house, knowing that it contained both Israeli civilians and Palestinian militants, "even at the cost of civilian casualties."

Relatives of some of those killed have demanded a probe into the potential deaths of some of these hostages from friendly fire, including one incident in which an Israeli tank fired at a house full of hostages.

On 7 October, as Israeli Doron Katz-Asher and other members of her family were being transported from the Nir Oz kibbutz on a tractor to be taken as hostages by Palestinian militants, the IDF fired on them to stop the tractor reaching Gaza; her mother Efrat Katz died from a bullet. Doron Katz-Asher was held hostage in Gaza for 49 days before being released during the ceasefire in late November. On 5 April 2024 it was announced that an IDF investigation found high credibility that Katz was likely killed by friendly fire.

On 7 October, Ofek Atun and his girlfriend Tamar escaped from the Re'im music festival massacre and attempted to enter kibbutz Alumim, which was also attacked, to seek refuge. Members of the kibbutz's security squad and a resident soldier mistook them for militants and opened fire, killing Atun and wounding Tamar.

According to the Israeli military, since the ground invasion of Gaza beginning on 29 October, an average of two to six soldiers were killed each week from friendly fire for a total of 18 soldiers out of 170 killed as of 1 January 2024. By 26 January the number of IDF troops killed in friendly fire incidents had been increased to 36 out of 188 soldiers reported as killed. They were a part of the about 17% of soldiers war-related deaths that were classified as accidents. On the six month anniversary of the 7 October attack in April 2024, the IDF published data on their engagements which included casualty numbers. Per the report 41 soldiers of the 604 killed since the start of the war were the result of operational accidents which included friendly fire.

Of the deceased some were killed by Israeli airstrikes, shrapnel from their own explosives, being run over by Israeli armored vehicles, and mistakenly identified and hit with tank fire, shelling and/or guns. These numbers do not take into account injuries resulting from friendly fire, but the IDF has indicated that they have had reports of those. Israeli hostages, who were freed by Hamas on 5th December 2023, convened with Benjamin Netanyahu's war cabinet. They asserted that Israeli helicopters intentionally targeted them as they entered Gaza during the Hamas attack on Israel on 7th October. Furthermore, they reported enduring continuous shelling from the Israeli military throughout their stay in the region.

The transparency of Israel's disclosure regarding friendly fire fatalities has made them subject to additional scrutiny, as many nations do not make such information public.

In early December 2023, three Israeli hostages died in an IDF airstrike on the Gaza city apartment where they were being held.

On 15 December 2023, IDF soldiers shot dead three Israeli hostages who were waving a white-flag in Shuja'iyya, Gaza.

After the IDF rescue operation in the Nuseirat refugee camp on 8 June 2024 which resulted in the rescue of four hostages taken during the Re'im music festival massacre, Hamas reported that along with heavy Palestinian casualties the IDF's operation resulted in the death of at least three Israeli hostages. The IDF has reportedly dismissed the reports of these hostages deaths, calling it a "blatant lie".

In August 2024, rescued hostage Noa Argamani reported that she had suffered injuries due to Israeli military airstrikes that causes a wall to collapse on her, while she was in held in Gaza.

On 8 January 2024, Israeli combat engineers were reportedly prepping to demolish a Hamas facility. A nearby tank crew mistakenly opened fire, leading to an electricity pole collapsing and setting off the explosives. Six soldiers lost their lives, and 14 others sustained injuries in the blast.

On 28 April 2024, two Israeli reserve soldiers in Gaza were killed by an IDF tank shelling a building in the Netzarim corridor where a group of Israeli soldiers were staying. The incident took place amid an exchange of fire with Hamas operatives in the area.

On 15 May 2024, five Israeli paratroopers were killed after being shelled by an IDF tank believing them to be Palestinian combatants.

Retired US Navy admiral and former supreme leader of NATO forces, James Straridis cautioned that the IDF had a very high friendly fire rate, even in a dense urban setting while speaking to reporters. Atlantic Council fellow and military intelligence expert Alex Plitsas cautioned that due to the fog of war, while any friendly fire instances are cause for concern, it was difficult to discern or reflect on if highlighted broader issues with the IDF and their tactics. Some experts such as retired US Lieutenant General Sean MacFarland highlighted the urban combat, lack of evacuation, and poor building quality due to the blockade which could cause higher numbers of friendly fire. While others such as Avner Gvaryahu of the IDF veterans organization against the occupation, Breaking the Silence stated its due to a policy of "very loose rules of engagement".

The sibling of one of the engineers killed in the 8 January incident, claimed the cause of his brothers death was a freak accident and he did not blame the soldiers involved as they were under large amounts of pressure and it was their duty to protect the engineers.

On 17 October 2023 a large explosion occurred in the parking lot of the Al-Ahli Arab Hospital in Gaza City, where a large number of displace Palestinians were sheltering. The cause of the explosion has been contested and various independent investigations into the explosion have produced a tentative explanation however due to the inability to investigate the physical evidence or conduct interviews due to on going war nothing has reached consensus. However, the majority of the investigations point to an errant rocket launch from within Gaza, which caused the death of between 100-342 people killed as the death toll is also contested.

In July 2024, there were reports that a Hamas missile had hit a school in Nuseirat.

Rockets fired by Palestinian groups at Israel have historically sometimes fallen within the Gaza strip itself. According to Israeli military data, 10% and 20% of launched rockets can be considered failed launches.

On 30 November 2023, In the Givat Shaul shooting in Jerusalem, two Hamas-affiliated militants from Sur Baher killed three and wounded sixteen Israeli civilians. The gunmen were killed by Yuval Castleman, an Israeli bystander who shot one of the gunmen. After two IDF soldiers arrived on the scene, one of them thought that Castleman was one of the gunman and he was fatally shot. Witness testimony alleges that Castleman raised his hands and shouted "I'm Israeli, do not shoot." Later testimony from the responding IDF soldier claimed that he did not hear Castleman speak.

• List of friendly fire incidents