CMF is governed by the General Assembly comprising of 27 members including SKBBL and MIFAN (51 % female and 49% male) and policy guided by the nine directors of the board chaired by Ganesh Bahadur Thapa, former governor of the central bank. The general assembly is an apex body of the organization, which meets once in a year. The number of assembly meetings may be increased as and when require. The board of directors directs the management on policy and guidelines for the effective operation of the organization, programs and projects. The board is elected every four years from among the shareholders of the organization. Gender sensitiveness, trust building, cooperation, learning, performance and inclusiveness are the key features of the governance of CMF.
The CEO heads the management of CMF and is responsible for participatory decision making in regards to the policies, objectives and strategies of the organization. The CEO leads the team of policy and operation in co-operation with the team of each thematic area of strategy including program, administration and finance departments. The management team develops new programs and proposals in consultation with CMF partners. Based on the CMF's strategic plan and policy guidelines, the program department prioritizes issues and develops program and projects accordingly. The central office acts as the principal administrative and coordinating body of the organization.