GAFCON is led by a Council of Primates, set up in 2008 at its meeting in Jerusalem.  It is now supported by the GAFCON Guarantors who ensure continuity of vision, strategy and resources and the GAFCON Trustees who monitor legal and operational compliance.

The Primates Council is served by a Secretariat led by the General Secretary, Archbishop Ben Kwashi and includes the Operations Manager, Membership Development Secretary, the Communications Manager and the Director of the GAFCON Bishops Training Institute.  Global co-ordination is achieved through Liaison Officers in GAFCON affiliated Provinces and elsewhere through a growing network of regional branches.