Alexandria University is administered through the University Council headed by the University President and with the membership of: three 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.

Administration of Alexandria University is done through the main offices including the President Office and Vice-Presidents Offices.