The Principals of the Mechanism are the President, the Prosecutor, and the Registrar, common to both branches of the Mechanism.

The President is appointed by the UN Secretary-General after consultation with the President of the UN Security Council and the Judges of the Mechanism. The Prosecutor is appointed by the UN Security Council on nomination by the UN Secretary-General. The Registrar is also appointed by the UN Secretary-General.

The President acts as the institutional head of the Mechanism. She is responsible for the overall execution of the institution’s mandate, and for representing the Mechanism before the UN Security Council and the UN General Assembly. She presides over the Chambers—the judicial organ of the Mechanism—and is responsible for appointing Judges to cases as required. The President of the Mechanism shall also serve as a Judge in, and presides over, the Appeals Chamber.

The Prosecutor is responsible for the investigation and prosecution of persons covered by Article 1 of the Statute of the Mechanism. The Statute provides that the Prosecutor “shall act independently as a separate organ of the Mechanism. He or she shall not seek or receive instructions from any government or from any other source”.

The Registrar leads the Registry, which provides administrative, legal, policy and diplomatic support to the Mechanism's operations, and assists the Chambers and the Office of the Prosecutor, in the performance of their responsibilities through the provision of support services.

The current Principals of the Mechanism are Judge Graciela Gatti Santana (President), Serge Brammertz (Prosecutor), and Abubacarr Tambadou (Registrar).