Alexandria University is administered through the University Council headed by the University President and with the membership of: four Vice-Presidents, Deans of all the Faculties and Institutes of the University, and four members with expertise on university education; appointed for two years liable to extension, after a resolution taken by the University President and after members of the Council state their opinion. The Secretary General of the University attends all Council meetings as Secretary of these sessions and takes part in the 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.