ARUA is currently governed through a Board of Directors which is made up of the 16 Vice Chancellors of member universities. The Board is expected to meet annually and to be concerned with general policy and oversight of programmes and operations, while leading the development of strategic objectives.
Six of the members of the Board constitute an Executive Committee, which is scheduled to meet quarterly. The Committee is required to take responsibility for carrying out the oversight responsibilities of the Board on a more regular and frequent basis. Apart from the Chair and Co-Chair of the Board, the remaining four members of the Executive Committee represent the different sub-regions that are reflected by ARUA universities.
Managing the affairs of ARUA on a day-to-day basis is the Secretary-General of the Alliance. The Secretary-General reports to the Board through the Executive Committee. He is assisted by a Secretariat currently located at the University of the Witwatersrand. By the initial support provided for the start-up of ARUA from the Kresge Foundation and Carnegie Corporation of New York, the Witwatersrand University manages the financial resources of ARUA and accounts for these to the funding agencies.
The current Board Chair is Professor Abel Idowu Olayinka, Vice Chancellor of University of Ibadan. Professor Adam Habib, Vice Chancellor of University of Witwatersrand is the Co-Chair.