The MFDP is headed by a Minister, appointed by the President, with the consent of the Senate. As administrative head of the MFDP, the Minister provides broad strategic and policy direction for the running of the institution. The Minister is further charged with formulating, institutionalizing and administering economic, development planning, fiscal and tax policies.

The office of the Minister also oversees a number of core administrative units including Legal and Internal Audit. In addition, the office also has oversight over some specialized units including the Public Finance Management Reform Unit, the EU Authorizing Office and the ECOWAS National Unit.