The UAPS Secretariat, which serves as the central administrative unit of the Union, is based in Accra, Ghana. Initially established in Addis Ababa, the Secretariat remained there until 1987, when it was relocated to Dakar, Senegal.

Since November 2006, it has been situated in Accra and is currently located on the 3^rd Floor of International House at the University of Ghana, Legon, Accra.

The current Secretariat staff includes an Executive Secretary (ES); a Research and Programs Manager (RPM); Editorial Assistant, Journal of African Population Studies  (JAPS); an Administrative Officer and an Administrative Intern.

UAPS also recruits temporary (ad hoc) staff as needed, particularly during major conferences.