The management structures of EDCTP include a European Economic Interest Group (EEIG-EDCTP), the legal entity for implementing the programme and managing the funding. The EEIG consists of:

• A governing body, the General Assembly, in which all participating European Member States are represented
• An executive body, the Secretariat, which assures the day-to-day management.

Partnership structures external to the EEIG, which comprise:

• The Partnership Board (PB), a panel of independent scientific experts that develops the strategic planning for EDCTP
• The Developing Countries Coordinating Committee (DCCC), an advisory board of senior African scientists and policy makers that  ensures the input and commitment of  African countries and researchers.

The Partnership structures and the European Commission hold permanent seats in the EEIG Assembly. The remit and function of each body are determined in the EEIG statutes and the Internal Regulations.