SEEU Faculties are organizational units within the University and operate through the Faculty Council and University policy framework approved by the University Board or Executive Committee. SEEU has five faculties: Faculty of Contemporary Sciences and Technologies, Faculty of Languages, Cultures and Communication, Faculty of Law, Faculty of Public Administration and Political Science and Faculty of Business and Economics.
The Mission of the University is defined in the Statute (December 1, 2008), it seeks excellence in teaching and research within the higher education system in the Republic of Macedonia, by offering equal opportunities for all based on impartiality and merit. One of the key elements of the mission of the University includes active cooperation with universities in the Republic of Macedonia as well as with the international universities.
The main aim under which the university is governed and managed is to contribute to higher education in the Albanian language, through a mutual interethnic understanding and aims to provide a multilingual and multicultural approach to teaching and research by developing study programmes according to broad European and international standards.
University governing bodies are the Board of the University, the Rector, University Senate and the Rector's Council.
South East European University is ranked second in the national level among 19 universities of the Republic of Macedonia. This ranking was carried out by the external evaluator, the Shanghai Jiao Tong University.