Prior to Nimeiri's consolidation of the court system in 1980, the judiciary consisted of two separate divisions: the Civil Division headed by the chief justice and the Sharia Division headed by the chief qadi. The civil courts considered all criminal and most civil cases. The sharia courts, comprising religious ÍÍÍÍjudges trained in Islamic law, adjudicated for Muslims matters of personal status, such as inheritance, marriage, divorce, and family relations. The 1980 executive order consolidating civil and sharia courts created a single High Court of Appeal to replace both the former Supreme Court and the Office of Chief Qadi. Initially, judges were required to apply civil and sharia law as if they were a single code of law. Since 1983, however, the High Court of Appeal, as well as all lower courts, were required to apply Islamic law exclusively. Following the overthrow of Nimeiri in 1985, courts suspended the application of the harsher hudud punishments in criminal cases. Each province or district had its own appeal, major, and magistrates' courts. Serious crimes were tried by major courts convened by specific order of the provincial judge and consisted of a bench of three magistrates. Magistrates were of first, second, or third class and had corresponding gradations of criminal jurisdictions. Local magistrates generally advised the police on whether to prepare for a prosecution, determined whether a case should go to trial (and on what charges and at what level), and often acted in practice as legal advisers to defendants.

In theory the judiciary was independent in the performance of its duties, but since 1958 the country's various military governments have routinely interfered with the judicial process. For example, in July 1989 the RCC-NS issued Decree Number 3, which gave the president the power to appoint and dismiss all judges. Under the authority of this decree, Bashir dismissed scores of judges, reportedly because they were insufficiently committed to applying the sharia in their decisions, and replaced them with supporters of the NIF. One of the most extensive judicial firings occurred during September 1990, when more than seventy judges were dismissed. The effect of these actions was to make the judiciary responsible to the president.

In November 1989, the RCC-NS established special courts to investigate and try a wide range of violations, including particularly security offenses and corruption. The special security courts handled cases that dealt primarily with violations of the emergency laws issued by the RCC-NS. The special corruption courts initially investigated charges that the state brought against officials of the Sadiq al Mahdi government, but since 1990 they have dealt with cases of embezzlement, foreign-currency smuggling, and black market profiteering. Critics charged that there was a lack of due process in the special courts and that the regime used them as a means of silencing political opponents. Judges sitting in the special courts included both civilians and military officers.

Data as of June 1991