Pursuant to the provisions of the Law and Bylaws, ANUBiH is composed of six departments established in line with selected branches of sciences and arts. Each department is headed by a secretary, elected by the department members and verified by the ANUBiH Assembly. The activities of departments are coordinated by the Assembly and the Presidency of the Academy.

Departments are authorized to form working groups (committees and commissions) which initiate study and evaluate various aspects of scientific and artistic activities. The working groups consist of ANUBiH members as well as other prominent persons from the relevant fields. The working groups are chaired by members of the Academy.

Within ANUBiH, i. e. its departments, there are centers and committees which operate as special organizational units. A center as a unit of mutual interest, can be established by more departments.