Of the twelve universities of which Øresund University is comprised, four are Swedish and eight are Danish. The number of Danish and Swedish students, however, is about the same. Øresund University is directed by the vice-chancellors of the member institutions who meet in the so-called 'vice-chancellors conference'. The conference meets once annually.

The chairmanship alternates between Swedish and Danish vice-chancellors. During 2007, Göran Bexell, the vice-chancellor of Lund University is chairman and Ralf Hemmingsen, the vice-chancellor of the University of Copenhagen is vice-chairman. The executive committee consists of six vice-chancellors. Apart from the chairman and the vice-chairman Lennart Olausson (vice-chancellor of Malmö University), Poul Holm (vice-chancellor of Roskilde University) and Finn Junge Jensen, (vice-chancellor of CBS) are current members.

The secretariat of Øresund University is located at Lund University and at the University of Copenhagen. The head of the secretariat is Bengt Streijffert who leads a team of another eight people. A few of these manage general matters within Øresund University while others work for the Øresund University platforms for the Øresund Study Gateway or the Øresund Summer University.