The Prosecution in Judea and Samaria was established in accordance with the Security Provisions Order and is headed by a regional Prosecutor. The Judea and Samaria Prosecution services include a military prosecutorial office in both Judea and Samaria, the military appeals prosecutor's office and an office dedicated to administrative detention orders. Prior to Disengagement from the Gaza Strip in 2005, the unit was also responsible for prosecuting cases in that region.

The Prosecution offices in Judea and Samaria manage the Criminal process from start to finish. The officers in the unit instruct investigatory bodies, submit indictments and manage criminal proceedings in many cases that concern security offences relating to hostile actions. Most cases are relate to some form of terrorist action, which were planned and/or carried out against Israel and its citizens, such as suicide bombings, shootings and membership and association with terrorist organizations. The Criminal process starts with an opening of an investigation and the gathering of evidence. The materials gathered are then transferred to the officers of the unit, who evaluate the evidence and decide whether to submit an indictment or close the case for a lack of evidence or a lack of public interest. In most terror related crimes, the prosecution requests the detention of the defendant without bail. Cases that continue to trial are conducted in accordance with the rules of evidence under Israeli law. Decisions of the court of first instance may then be subsequently appealed by either side to the Military Court of Appeals.

In addition to the above mentioned proceedings, various other offences are handled related to civil unrest, stone Molotov cocktail throwing , unlawful entry and stay into Israel and property offences found within the military commander's range of interest and jurisdiction.

The Prosecution's work is conducted in full cooperation with the Israeli police and various additional regional security bodies. Amongst the complicated and sensitive cases handled by the prosecutorial teams are those concerning the dispatching of suicide bombers, the cases involving the lynching of two IDF reserve soldiers in Rammalah and other deadly terrorist attacks within Israeli settlements in Judea and Samaria. Likewise many senior members of terrorist organizations in the region were have been tried by these courts.