AKHS is organised into national service companies in Afghanistan, India, Kenya, Kygyzstan, Pakistan, Syria, Tajikistan, Tanzania, and Uganda. The Head Office is located within the Delegation of the Aga Khan Development Network in Gouvieux, France and and at AKDN offices in Geneva, Switzerland, co-ordinates the activities of the service companies through five-year plans, ten-year projections, annual budget submissions, and the provision of technical assistance.
They are also linked internationally through network-wide strategies for regional geographies, such as Central Asia and East Africa, as well as in human resource development, hospital management, nursing development, and primary health care.