EUREKA's organisational structure is composed of four main bodies:

Ministerial Conference: a minister from each EUREKA member country and a Commissioner from the European Commission meet once a year at the Ministerial Conference, the political body of EUREKA. The Ministerial Conference announces the new projects endorsed during the year. Ministers also take decisions on the further development of EUREKA.

High Level Group : meets three or four times a year. Each EUREKA member appoints one representative to this group, which takes decisions on the management of EUREKA and prepares policy discussions for the Ministerial Conference. High Level Representatives are usually named by the Ministry responsible for EUREKA.

National Project Coordinators : The National Project Coordinators are the direct contact with EUREKA. They are responsible for contacts with project participants and potential project participants in each member country. They meet four or five times a year and are also responsible for project generation. They advise on funding and smooth the way for setting up a project.

The EUREKA Secretariat in Brussels is the central support unit, managing the EUREKA project database and undertaking marketing, communication and network development activities.