While the PAU considers the basic principles of the Constitutive Act of the AU, Agenda 2063 and the relevant AU strategies, the PAU Statute of January 2016 stipulate a set of principles that are elaborated and concretized in the PAU Strategic Plan 2020-2024. The Statute state the principle of academic freedom, accountability and autonomy. Furthermore, the PAU's basis lies on the following principles: 

• Focus on Excellence
• Pan African Integration
• Social Inclusion, Diversity & Gender
• Sustainability
• Relevance