CEEPUS is based on lean management. The highest ranking decision making CEEPUS body is the Joint Committee of Ministers that meets once a year and takes all strategic decisions. Coordination, evaluation, program development and advertizing are the main tasks of the Central CEEPUS Office (consisting of only two persons). Each country has a National CEEPUS Office in charge of national implementation. In order to avoid setting up new administrative bodies, the National CEEPUS Offices are integrated into already existing structures, usually national agencies.

FInancing

With CEEPUS, there is no transfer of funds: There is an internal currency of "one scholarship month" instead. Each country pays its INCOMING students and teachers and has to pledge at least 100 scholarship months per academic year. Croatia has pledged 450 scholarship months for the academic year 2014/2015. The CEEPUS Agreement specifies that these grants be comprehensive grants linked to the local cost of living.