The functions of the Fund are administered by the Secretariat.  Functionally, there are six pillars addressing six core departments of fund management, programming, monitoring & evaluation and policy & strategy and corporate services, together with a procurement & disposal of assets unit and an internal audit department reporting directly to the Board.

The Executive Director and the departmental managers constitute the Fund Management Committee, which is the top policy and administration organ reporting to the Board. The design of the structure was informed by the desire to remain lean so as to achieve economy and efficiency.