The Executive Secretariat assures the day-to day activities of the EEIG, runs independent peer review systems, supports the Partnership Board's policy development and networking, supports the work of the EEIG Assembly, Developing Countries Coordinating Committee (DCCC), and European networking; handles liaisons and negotiations with partners, oversees funded programmes, and maintains operational and financial control systems.

The Main Office of the EEIG Executive Secretariat is situated in The Hague, the Netherlands. The Secretariat established a second office in Cape Town, South Africa, which represents EDCTP in Africa, and promotes the participation of developing countries in EDCTP. It provides support to activities of EDCTP constituencies in Africa, in particular the DCCC and the High Representative.