The CHAK governance structure is defined by its Constitution (Click here to view the CHAK Constitution).

Annual General Meeting
CHAK’s supreme authority, the AGM, is composed of all registered members and meets annually in April.

Board of Trustees
CHAK has a Board of Trustees composed of seven senior church leaders from member churches who are mandated by the Constitution to hold in trust all the assets of the Association.

The Board of Trustees is made up of senior church leaders of national stature appointed by the Annual General Meeting (AGM) to serve a renewable six-year term. CHAK's Constitution requires that the trustees be either serving or retired senior church leaders from CHAK member churches. The Board of Trustees meets annually.

The trustees are responsible for overall mission and strategic direction of the organisation. They also approve infrastructure development and investments. The current Board of Trustee members are as follows:

• Rt. Rev. Charles Asilutwa – Anglican Church of Kenya (ACK)
• Rev. Dr. Robert Lang’at - Africa Gospel Church 
• Rt. Rev. Joseph Wasonga – Anglican Church of Kenya (ACK)
• Rev. Prof. Zablon Nthamburi – Methodist Church in Kenya (MCK)
• Rt. Rev. Julius Guantai Mwamba – Presbyterian Church of East Africa (PCEA)
• Rev. Bishop Paul Manyara – Africa Inland Church (AIC)
• Dr Samuel Makori – Seventh Day Adventist (SDA) Church
• Dr Samuel Mwenda – General Secretary

Executive Committee (EXCO)
The Executive Committee (EXCO) is the executing arm of the AGM with the mandate to formulate policies, approve plans and monitor program implementation as well as accountability. EXCO members are elected by the AGM to serve a term of two years which is renewable to a maximum of six years.

Currently, EXCO members are as follows:

• Rt. Rev. Charles Asilutwa - Chairman
• James Maina - Vice-Chairman
• Christine Kimotho - Treasurer
• George Opundo - Vice-Treasurer
• Joel Jamhuri - RCC Chairman Central/Nairobi/South East/Coast Region
• Ruth Nabie - RCC Chairman Western/North Rift Region
• Rev. Samson Musyimi - RCC Chairman Eastern/North Eastern Region
• Erick Lang’at - RCC Chairman Nyanza/South Rift Region

CHAK Secretariat
The Secretariat is led by the General Secretary and is structured into three departments:

• Health Services
• Institution & Organisation Development
• Financial Management and Administration

These departments are supported by ICT, HR and M&E Units.