Alexandria University is administered through the University Council headed by the University President, who is appointed by a Presidential Decree, with the membership offour Vice-Presidents appointed each by a Prime Minister's Decree, Deans of all the Faculties and Institutes of the University, and four members with experience on university education. These latter are appointed for two years liable to extension, after a resolution taken by the University President and the approval of the members of the University CounciL. The University Secretary General attends all Council meetings as the secretary of the sessions and takes part in discussions.

The President runs the University academically and administratively according to the bylaws and the regulations approved by the Supreme Council of Universities. He serves as the Chief Executive and Operational Officer of the University, and is directly responsible of the management of all University affairs to the University Council, the Supreme Council of Universities, and the Ministry of Higher Education. The President may delegate responsibility or authority to other Council members, or individuals in the University community.