The University of Antananarivo is governed by Decree 565-2002 of 04 July 2002. It is administered by a Board of Directors (deliberative body) and headed by a president (executive body). It also has a Scientific Council of the University composed of the President and the Deans / Directors of the Institutions. This Council gives its opinion on everything related to Training and Research.

Each Institution is administered by a Council (Faculty Council or School Council), and is headed by a Dean or Director. This Faculty or School includes, in addition, a Scientific Council, a College of Teachers and a College of Departments. Vocational training courses are now established within the establishments.

The Board of Directors of the University of Antananarivo's mission is to:

• Define the University's development policy within the framework of the national policy in force.
• Review and approve the University's budget and accounts that must be in balance
• Accept donations and legacies

• Define the main activities of the University
• Define the conditions of access and continuation of studies at the University
• Ratify agreements with other national and foreign organizations

With regard to pedagogy and research, a Scientific Council has been set up to advise on:

• any questions relating to pedagogy and research
• the main activities of the University
• the conditions of access and continuation of studies in the University
• agreements with other national or foreign bodies
• Orientation, implementation and coordination of research programs and activities as well as doctoral and post-doctoral training within the University
• The distribution of research credits
• The teacher training plan, the work or the activities of the teachers