The Court was established in 1994 upon the adoption of the current COMESA Treaty and it assumed the overall jurisdiction of the previous judicial bodies that existed under the Preferential Trade Area of the Common Market for Eastern and Southern Africa (PTA). The judicial organs under PTA were:
- The PTA Tribunal whose function was to ensure proper interpretation of the provisions of the Treaty as well as to adjudicate upon all disputes between Member States that would arise from the interpretation and application of the PTA Treaty;
- The PTA Administrative Appeals Board whose jurisdiction was to adjudicate upon disputes between the PTA and its staff arising from the interpretation and application of the PTA Treaty, Staff Rules and Regulations and Terms and Conditions of Contracts of Employment of Staff; and
- The PTA Centre for Commercial Arbitration which was responsible for facilitating international arbitration and conciliation of private commercial disputes. The Centre was based in Djibouti and operated under the auspices of the PTA Federation of Chambers of Commerce and Industry.
The Court operates as an independent organ of the Common Market and comprise of two Divisions, the Appellate Division which is headed by the President and the First Instance Division, which is headed by the Principal Judge, the day-to-day operations of the Court are done by the Registrar of the Court under the supervision of the Judge President and is assisted in his duties by other Registry and Administrative Staff.