PPD has its Secretariat headed by the Executive Director, which is located in Dhaka, Bangladesh. It has a Regional Office in Kampala, Uganda headed by a Regional Director to coordinate South-South program activities in Africa. It has a Program Office in Taicang, China headed by a Director to organize its South-South Capacity Development activities for professionals from the member states. In order to represent PPD in the United Nations, PPD maintains a Liaison Office to the UN in New York headed by PPD Permanent Observer to the United Nations.
PPD also has a country coordinating mechanism involving one senior government official in each member state known as Partners Country Coordinators (PCCs) to coordinate South-South program activities with different sectors within the country, among other member countries and with the PPD Secretariat, regional offices and its affiliates.