CCM Nepal has a Committee composed of 17 voting members representing different sectors and constituencies; the Government of Nepal (GoN), civil society/NGOs working in HIV/AIDS, TB, and Malaria, people living with or affected by HIV/AIDS, TB, and Malaria; community organizations; the private sector; professional associations; research institutes, universities, media and international agencies including multilateral or bilateral agencies, international donors and international NGOs.The Executive Secretary of the CCM Secretariat is a non-voting member of CCM Nepal.

CCM Nepal has an Executive committee of five members with a chair and vice-chair who are assisted by an executive secretary. The Executive Secretary executes the day-to-day tasks and facilitates various decisions of the CCM. The hierarchy of authority in the CCM is as follows: CCM; Executive Committee; Chair; Vice Chair. Within this hierarchy, any party can be overruled by parties higher in the hierarchy. The current CCM Chair is from the Ministry of Health and Population- Government of Nepal and the Vice-Chair was from the Civil Society.