The Fourth Ordinary Session of the Conference of Ministers of Education of the African Union (COMEDAF IV) held in Mombasa in November 2009, endorsed the PAU as an academic network of already existing post-graduate and research institutions.

The structure of the PAU includes one Rectorate as overall coordinating office; five Institutes, one in each geographic region, as coordinating hubs for each thematic area; up to ten Centres from around Africa in each thematic area, networked to the relevant thematic Institute or hub.

Management
The PAU shall be managed by the following three organs:

The PAU Council: This council shall be the governing body responsible for PAU and its functions. The members of the Council shall include representatives of major stakeholders, among them academics, community leaders, and representatives of the Regional Economic Communities and of the private and industrial sectors. The Association of African Universities and the African Academy of Sciences will also play a major role. The Council shall be responsible for ensuring adherence to the vision of the African Union, and to the imperatives of excellence, quality and relevance of PAU’s policy and practice

The Rectorate: The Rectorate shall be the executive body of PAU and shall be responsible for the overall planning, monitoring and coordination of the Institutes and Centers. The Rectorate shall be headed by a Rector/ Vice Chancellor who shall exercise a supervisory role over internal and external university communication and co-operation, and shall report to the Conference of Ministers of Education of the African Union through the Commission of the African Union.

The Senate: The Senate shall have primary responsibility for all academic affairs of PAU. The composition of the Senate shall include, among others representatives of Vice Chancellors and Directors of Institutes and Centres; and representatives of Privileged Partners and students. The Senate shall be convened and chaired by the PAU Rector/Vice Chancellor