The Christian Council of Lesotho is run by a nominated Executive Committee with its own elected Chairperson and Deputy and appointed General Secretary. The Executive Committee is responsible to the Annual General Conference. The Heads of member Churches are Trustees of the Council. The Council is aided by programmatic ecumenical commissions and Regional Committees reflecting the current membership of the CCL.
The Council is legally registered under societies Act of 1966 and it is a member driven organization. It enjoys Legal status of an autonomous body having perpetual succession and power to own property in its own name. The Council as corporate body possesses all such powers as are requisite for carrying out its objectives as provided in the societies Act of Lesotho of 1966. It is supported by members through subscription fees, friends, volunteers and partners through gifts and response from appeals and proposals.