In spring 2000, OSCE High Commissioner for National Minorities initiated discussions for establishment of a new university in the Republic of Macedonia, which was supported by international donors.
Following the adoption of the Law on Higher Education by the Parliament of the Republic of Macedonia, that allowed the founding of universities that are not related to the state and supported higher education in Albanian language. In late 2000, OSCE High Commissioner for National Minorities started the planning of the University. Construction work started in March 2001, and South East European University (SEEU) was opened six months later. In November 2002, the number of students was 2250, and in October 2003, the number of students was 3700.