Since the foundation of the University its fundamental mission has been to create and give access to knowledge of the highest level as well as to enable intellectual growth of those seeking to expand existing, and generate new knowledge.
With the beginning of its fourth year of operation, SEEU began setting up its profile as a higher education research institution. In December 2004, the University Board approved the university strategy on research, with responsibility for the implementation of the University action plan on research.During this period, five faculty research centres were constituted and Directors were appointed. These five faculty research centres together with other research entities as Institute of Environment and Health, Centre for Human Rights and Bioethics Unit represent the main research structure of South East European University. The University is gradually promoting programmes of research and scholarship linked to its mission of education at all three cycles defined by Bologna Process and contributing to the economic and social development of Macedonia and the region.
The Research Office is the university umbrella for all activities involving research and publications. The Research Office manages, administrates and monitors the overall technical administrative progress of the research at the university.
Up to date SEEU has developed 65 research projects from internal research funds, 29 TEMPUS projects as well as has been coordinator in other international research projects funded by FP7, RRPP, UNDP, ASO etc.
SEEU has published 86 titles including textbooks and reports of research projects across the range of its academic disciplines. By 2011 has published 10 issues of SEEU scientific journal SEEU Review, with different papers from SEEU staff and foreign authors in the frame of university collaboration.