The Association holds General Assemblies of members annually where the activities of the Association are discussed and future plans approved. The General Assembly is the highest decision making body with the responsibility of providing an overall policy framework. An Executive Committee elected by the General Assembly and serving for three years provides leadership. All members of the Committee serve without pay. It has a secretariat with employed staff who manages the day to day activities of the Association.
The Ethiopian Economic Policy Research Institute, which is a subsidiary of the Association is organized under four research divisions namely, Agriculture and Rural Development Division, Trade and Industry Division, Social and Human Resource Division and Macroeconomic Division. Each division is staffed with at least one full time senior researcher and one researcher.