AKHS is organised into national service companies in Afghanistan, India, Kenya, Kyrgyzstan, Pakistan, Syria, Tajikistan, Tanzania and Uganda. The Head Office is located at the AKDN offices in Geneva, Switzerland. It coordinates the activities of the service companies through five-year plans, ten-year projections, annual budget submissions and the provision of technical assistance.

AKHS is also linked internationally through network-wide strategies for regional geographies, such as Central Asia and East Africa, as well as in quality of care, digital health, virtual learning, climate change measures, population health, communications, human resource development and audit.

While strengthening its institutions and the links between them, each health service company joins government health services and other providers in building effective national health systems. AKHS and AKU manage 22 hospitals and more than 700 health centres.