The Conseil Supérieur de la Magistrature (Superior Judicial Council) is, according to Article 152 of the Constitution, in charge of managing the administration of justice. Its missions include making proposals for the appointment, promotion and dismissal of magistrates, and exercising disciplinary authority over magistrates.

It is composed of : 

• President of the Constitutional Court ; 
• Attorney General to the Constitutional Court; 
• First President of the Court of Cassation;
• Attorney General to the Court of Cassation; 
• First President of the Conseil d'Etat ; 
• Attorney General to the Council of State; 
• First President of the Military High Court; 
• Auditor General to the Military High Court; 
• First Presidents of the Courts of Appeal; 
• Procureurs Généraux près les Cours d'Appel; 
• First Presidents of the Administrative Courts of Appeal; 
• Procureurs Généraux près les Cours administratives d'Appel ;
• First Presidents of Military Courts ;
• Senior military auditors ;
• two judges per Court of Appeal, elected by all judges in the area for a three-year term;
• two prosecuting magistrates per Court of Appeal jurisdiction, elected by all magistrates in the jurisdiction for a three-year term;
• one judge for each military court;
• one magistrate per military court.

The Cour de Cassation (Court of Cassation) is the highest court in the ordinary court system, and as such has under its control the civil and military courts. Among the courts of the ordinary judicial system are the magistrates’ courts (tribunaux de paix), military courts, the Tribunal de Grande Instance, commercial courts, Courts of Appeals, and the Military High Court. In the ordinary court system, the Court of Cassation is the court of last resort. It hears appeals in cassation from the ordinary courts, but does not rule on the case itself, but on questions of law specifically referred to it. In addition, the Cour de Cassation is the court of first resort for criminal cases involving politicians and senior civil servants, such as members of the National Assembly and Senate, members of the Government (with the exception of the Prime Minister), and members of the Cour des Comptes. The ordinary court system is organized by the  Loi organique n° 13/011-B du 11 avril  2013 portant organisation, fonctionnement et compétences des juridictions de l'ordre judiciaire.

The Conseil d’Etat (Council of State) is the highest court in public and administrative matters (article 154 and 155). The Conseil d'Etat hears appeals against decisions of the administrative courts of appeal. In the absence of competent institutions, it hears claims for compensation for exceptional material or moral damage resulting from a measure taken or ordered by the authorities of the Republic.

The Constitutional Court has nine members. Three are appointed by the President of the Republic, three by Parliament, and three by the Conseil Supérieur de la Magistrature. One-third of the Court's members are replaced every three years. The main task of the Constitutional Court is to review the constitutionality of all legislation, including international treaties and agreements. It is also responsible for interpreting the Constitution. The Constitutional Court is also responsible for resolving conflicts of jurisdiction between the executive and legislative branches, the central state and the provinces, and the various levels of court. It also rules on election disputes. Its organization and functioning are set out in the Loi organique n° 13/026 du 15 octobre 2013 portant organisation et fonctionnement de la Cour Constitutionnelle.

Customary justice is not recognized as part of the country's legal system, but the Constitution does recognize customary authority in the country, provided it is not contrary to the Constitution, the law, public order or morality (article 207). There is virtually no interaction between traditional justice and the judicial system. Traditional justice in fact fills the gaps in the judicial system, in that many provinces have no ordinary courts. Because of the remoteness of the courts, a large proportion of the population, the majority in fact, turns to traditional justice mechanisms. Cases brought before traditional justice mechanisms mainly concern personal status (e.g. marriage and divorce) and property rights, notably inheritance and land ownership. It is important to note that the customary law resulting from this traditional justice varies from one community to another, and therefore has no general application across the territory.