The Board of Trustees are legal owners of CHAN who hold in trust the organizational assets and liabilities. The National Executive Council of CHAN, headed by the President, is the central policy-making and co-coordinating body of the organization. Operationally, the activities of CHAN are initiated from the Headquarters based in Jos, Plateau State. The Secretary General who is responsible for the day-to-day running of the organization, reports to the National Executive Council. Below the Secretary General, are a team of Directors, who have oversight responsibility for the various departments/units within the Organization. The Advocacy and Communication unit helps to coordinate all advocacy/MIS activities of CHAN. The Account/Administrative unit coordinates all accounts/financial and administrative Services of CHAN. The Audit unit is an appraisal unit established by Management for review of operations of the organization and reports to the NEC through the Secretary General;
For purposes of ensuring effective service delivery, CHAN operates a decentralized system of administration. Zonal Offices have been established in four locations. In the Northeast, Zone A with 7 states and zonal office in Numan, Northwest/central zone B with 12 states including the Federal Capital Territory Abuja and with zonal office in Jos, southeast, Zone C with 9 states with zonal office in Emekuku, Owerri, and South –West, Zone D with 8 states with zonal office in Ibadan. These zonal offices manage relationships with MIs as well as provide on-site support that MIs urgently require and refer other issues to headquarters for further action. To enhance the work of the organization, the MIs have been constituted into zonal and State committees through which they input into the decision-making process and act as channel for communication.