AEUA has a straightforward structure. At the centre of this organisation are its members: universities in Arab and European countries. A Board of seven members is elected by the membership and meets regularly. Under an independent Chairperson, three Arab and three European members form the Board. The Lutfia Rabbani Foundation and both the European University Association (EUA) and the Association of Arab Universities (AARU) are represented on the Board.
The AEUA Board is responsible for developing the Association's policy and work programme and for its implementation.