The future of Palestinians detained by Israel in the context of the Israeli–Palestinian conflict is considered central to progress in the Israeli–Palestinian peace process. Cases of prison sentences include the charges of terrorism or being a member of an "illegal terrorist organization", such as Hamas or, prior to the Oslo Accords, the Palestine Liberation Organization, but according to some accounts also the charge of political activism, such as raising a Palestinian flag.

In April 2022, there were 4,450 Palestinian security prisoners in Israeli prisons – including 160 children, 32 women, and over 1,000 "administrative detainees" (indefinitely incarcerated without charge). According to B'tselem, since the outbreak of the Gaza war on 7 October 2023, Palestinian prisoners with Israeli citizenship have been stripped of many of their rights. It further found that abuse of detainees is so institutionalized that the prisons should be called 'torture camps'.

In December 2011, 4,772 Palestinian security prisoners were serving terms in Israeli prisons. Of these, 552 were sentenced to life terms. By July 2024, there were 9,623 Palestinians incarcerated by Israel, 4,781 in administrative detention, for alleged security reasons.

The Israeli military court system for the occupied territories, modeled partially on the British military court system set up in 1937, was established in 1967, and had been called the institutional centerpiece of the occupation, and within it West Bank Palestinians are treated as "foreign civilians".

The measures it applies, combining elements of colonial administration and martial law, cover not only incidents involving recourse to violence but many other activities, non-violent protests, political and cultural statements and the way Palestinians are allowed to move or associate with each other.

Some of the problematic facets of the system Palestinian prisoners are subject to are, according to sociology professor Lisa Hajjar, prolonged detention of suspects incommunicado, impeding a client's access to his lawyer, the routine use of coercion under interrogation to obtain confessions and the introduction of "secret evidence".

Hundreds of thousands of Palestinians have been put on trial since 1967. According to Saree Makdisi the cumulative total of Palestinians imprisoned by Israel reached 650,000 in 2005. Of these, according to Tamar Pelleg-Sryck (2011), tens of thousands have been subjected to administrative detention. The incarceration rate was the highest in the world during the First Intifada (1987–1992) – and their conviction rates varied from 90 to 95%, being for the most part secured by plea bargains in 97% of cases. According to Red Cross statistics, in the first two decades of the occupation, from 1967 to 1987, one in three Palestinians, about 500,000, were detained by Israeli forces, and on any given day the courts would be crammed with "children in handcuffs, women pleading with soldiers, anxious people thronging lawyers for information." After the Oslo Accords, courts in Palestinian towns were withdrawn to Area C, causing greater difficulty for lawyers and family of the defendant to get access to the tribunals because of the permit system.

The specific practice of administrative detention was initially introduced by the British to subdue Palestinians, but was then increasingly applied to cope with behavior by Jewish political activists and suspected members of Jewish paramilitary organizations, an extension vigorously opposed by Jewish settlers at the time and one which Jewish lawyers in July 1936 argued should be repealed. Dov Yosef likewise argued in 1948 that the practice abolished the writ of habeas corpus and had led to the improper incarceration by the British of numerous Jewish activists. The state of Israel, on securing independence however, retained this body of regulations on the new state's statute book. Article 111 therein enabled military commanders to arrest and detain anyone, without public reasons given or the laying of formal charges or trial, for periods of up to one year, though a provision exists for indefinitely extending any person detained under the order. The Fourth Geneva Convention permits detentions, and on these precedents the IDF promulgated its Article 87 of the Order Concerning Security Instructions, and applied it to cases where the rules of evidence of Israeli courts would not allow the suspect to be convicted. Egregious examples of the practice took place early in the occupation. Taisir al-Arouri, a Bir Zeit University professor of Mathematics, was arrested at night on 21 April 1974 and released on 18 January 1978, after suffering 45 months of imprisonment without trial or charges being laid, only after Amnesty International issued a public protest.