The Management Board comprises up to 9 Directors, including the Chairperson and the Chief Executive Officer. The Directors do not represent their individual countries, but the interests of the Alliance. The Association of African Universities (AAU) runs a process to appoint the Chairperson, who sits for a term of 3 years.

• Professor Zimani D. Kadzamira - Chairperson (ex oficio)
• Mr Albert Nsengiyumva - Deputy Chair
• Dr Iman Abuel Maaly Abdelrahman
• Professor Meoli Kashorda
• Professor Kohn Kondoro
• Dr Duncan Martin
• Ms Margaret Ngwira
• Mr Steve Song
• Eng. Dr Francis F. Tusubira - Acting CEO (ex oficio)

The current Management Board was elected at the 3rd Council of Members Meeting in Nairobi Kenya on 17th April 2009 for a 2 year term. The Term of of the Chairperson will expire in 2010.