The PAU is a continental academic, research and innovation institution based on the following guiding principles:
- Academic freedom, autonomy and accountability;
- Quality assurance;
- Strengthening existing African institutions at the graduate studies level to enable them to serve the whole continent;
- Promotion of African integration through the mobility of students, academic and administrative staff, as well as the development of collaborative research linked to the challenges faced by African countries;
- Excellence and international partnerships in academic and research activities;
- Institution of an appropriate framework and a conducive environment to enable the African Diaspora to contribute towards the development of higher education, research and innovation in Africa;
- Promotion of inter-disciplinary and multidisciplinary research programmes integral to policy making processes in Africa;
- Promotion and harnessing of productive linkages with the industrial sector for innovation and dissemination of new knowledge and technology;
- Strengthening of research particularly in the thematic areas of the PAU;
- Promotion of optimal use of Information and Communication Technologies for pedagogy, research and management;
- Promotion of gender equity at all levels and in all university functions; and
- Promotion of access to higher education for persons with disabilities.
The PAU shall take into account basic principles of the Constitutive Act of the AU, AU Instruments and Policies on Higher Education, Science, Technology and Innovation, Agenda 2063, the African Charter on Human and People’s Rights as well as other regional and international human rights instruments.