The GFCF was established in 2006, initially as a 3-year pilot project of WINGS (Worldwide Initiatives for Grantmaker Support) and jointly supported by the World Bank (Development Grant Facility), Charles Stewart Mott Foundation and Ford Foundation. Further sources of support were received through USAID (Global Development Alliance), W.K. Kellogg Foundation, TrustAfrica, Rockefeller Brothers Fund, King Baudouin Foundation, International Development Research Centre and others. In 2007, the GFCF embarked on a detailed feasibility regarding its establishment as an independent entity which concluded that the GFCF was filling an important gap in the institutional architecture of philanthropy. On this basis, the decision was taken to proceed with the GFCF as an independently constituted organization, registered in both the U.K. and South Africa.

The GFCF operates from an office base in Johannesburg, South Africa, with other staff members in Belgium, Nigeria, Uganda and the U.K. A global board oversees its operations. It maintains a small staff and works on the basis of key partnerships with other organizations to both resource and extend its work.