The ATJLF is governed by a Board of Trustees who provide overall oversight of the organisation, including the recruitment of the Director and other staff members. The organisation also has an Advisory Committee (AC) made up of seven people, including representatives of the two funding foundations. The Advisory Committee provides high level strategic programme direction of the fund. They also provide matrix management of the Director of the ATJLF Secretariat. The Advisory Committee also makes final decisions on award of grants.

The ATJLF comprises staff from different countries in Africa who work very closely with partners and grantees across the continent.