In its present form the body was created after the breakup of the SFR Yugoslavia and the end of the Yugoslav Wars.

Association facilitates the regional cooperation in the context of expansion of higher education sector caused by the establishment of new private and public universities (in addition to traditional schools with their existing institutional links).

Association helped in the exchange of experiences in the implementation of the Bologna Process at Balkan universities.

In addition to the bilateral meetings, conferences of the Balkan universities take place at changing member locations.

In 2016, the Rector of Trakya University Erhan Tabakoglu in Edirne has taken over the general secretariat of the association.