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 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 scientifically independent expert panel that develops the strategic planning of the EDCTP
• The Developing Countries Coordinating Committee (DCCC), which consists of representative African scientists and ensures the input and commitment of the African countries and researchers
• The European Network of National Programmes (ENNP), which consists of representatives of the European national programmes and develops proposals to coordinate and joint national activities and funding.

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