CLARION's organisational structure includes: the General Assembly of Members, the Board of Directors, the Management Committee and the Secretariat. The General Assembly meets annually, while the Board of Directors meets quarterly according to the Constitution, with additional meetings called whenever required. The General Assembly is the supreme organ of CLARION mandated with policy making.  It also approves policy decisions made by the Board.

The Management Committee is responsible for the day-to-day running of CLARION's affairs. The organ is answerable to the Board and implements policies and decisions made by the Board. The secretariat facilitates the day-to-day running of CLARION affairs, and its members are answerable to the Management Committee.