The Tanzania Commission for Universities (TCU) operates under a structured framework with the Commission as its supreme decision-making body. This governing board sets policies and strategic directions for higher education in Tanzania, while the Secretariat, led by the Executive Secretary (ES) who is Chief Executive Officer (CEO), is responsible for executing decisions of the Commission and managing daily operations of the institution.

To support its functions, the Executive Secretary is assisted by three Directors, each leading a specific directorate. The Directorate of Accreditation ensures universities meet the required academic and quality assurance standards. The Directorate of Admissions Coordination and Database Management coordinates the student admission process in institutions and higher education data management. Meanwhile, the Directorate of Corporate Services provides financial, administrative, and human resource support. These directorates are further supported by section heads appointed based on their expertise.