WAEON's organizational structure consist of a General Assembly and an elected Executive Council. The General Assembly is the supreme body of WAEON and consist of nominated representatives of all member organizations. The Executive Council is composed of seven (7) officers elected at large by the General Assembly. The officers of WAEON are as follows: Chairperson, two Vice Chairpersons (Francophone and Anglophone), Treasurer, and three other members. The Executive Council, amongst other functions, supervises the implementation of all WAEON's programs and activities.
The headquarters of WAEON is established in Accra, Ghana. The Ghana Center for Democratic Development (CDD-Ghana) currently serves as Secretariat for WAEON.