Under the policy of UNECA, the Chairman of the Governing Council of AFRIGIST is elected from among the members to serve for two consecutive meetings in rotation.

The organisational structure of AFRIGIST is as follows:

• The Directorate with the Executive as Chief Executive Officer of the Centre, assisted by a Deputy Executive Director.
• The Academic and Research Division, headed by the Dean of Academics and comprising the following Departments:
  • Department of Photogrammetry and Remote Sensing;
  • Department of Geographic Information Science;
  • Department of Cartography
• The Academic and Research Division has the following two (2) Units:
  • The ICT Unit;
  • The Library, Information and Publication (LIP) Unit.
• The Administration Unit, headed by the Head of the Administration;
• The Account Unit, headed by the Principal Accountant
• The Audit Unit; and
• The Consultancy Services Unit.