SEEU has, with the beginning of its sixth year of operation, also begun 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, the boards of the individual faculty research centre have been constituted and Directors have been appointed for each Faculty based research centre.
Dr. Dennis Farrington is the Pro-Rector for Research and International Cooperation and Diturije Ismaili is Head of Research Office.  As part of the strategy to improve research, the University has increased the research and development fund to 6% of the University’s budget.

The University is gradually promoting programmes of research and scholarship which are linked to its mission and in particular contributing to the economic and social development of Macedonia and the region, while not ignoring the element of research and scholarship purely for academic reasons.

The quality of research projects is assessed first through submission of proposals according to a template based on formal Regulations which set out clearly the required criteria. There is then discussion of draft proposals in the Research Committee, followed by an iterative process of amendment, re-submission and approval, with regular monitoring of the successful proposals by the Research Office. Finally, researchers present their conclusions in a way which can readily be disseminated outside the University through conferences, publication of texts or the SEEU Review.

The ability to generate external funds to support research projects is a major criterion in allocating University funds. Administrative support and assistance to the Faculty Research Directors is provided by the Research Office.