CHAK is a leading national Faith Based Organization (FBO) of Protestant churches' health facilities and programs from all over Kenya. Established in 1946, CHAK has the goal of promoting access to quality health care. The organization’s structure includes member health facilities and member programmes, governance organs which include a regional structure and the Secretariat based in Nairobi.

The organisation's core functions may be broadly categorized as
a) Health service delivery
b) Health systems strengthening
c) Governance and accountability 

CHAK's programmes and activities are guided by the six-year Strategic Plan 2011-2016 which has clustered the organisation's core functions into the following strategic directions:

• Health service delivery including HIV&AIDS programmes
• Health systems strengthening
• Governance and accountability
• Research, advocacy and communication
• Health care financing and sustainability
• Human Resources for Health (HRH) 
• Grant management

CHAK Secretariat is organized into three departments and one support unit under the leadership of the General Secretary. The Secretariat discharges the above core functions through various projects and programmes. 

The Annual General Meeting is CHAK's highest body of authority. It elects the Executive Committee (EXCO) which is responsible for formulating policies, approving operational plans, projects and budgets and ensuring regular financial and programmatic monitoring.

CHAK's national network of member health facilities is divided into four geographical regions, each of which is led by a Regional Co-ordinating Committee. CHAK's activities are coordinated centrally from the Secretariat in Nairobi.