Higher education and research represent the driving forces for economic and institutional change in both developed and developing countries all around the world. The countries of the Southern and Eastern Mediterranean (SEMCs) are not an exception from this case as they are making notable efforts to enhance the institutional reform of higher education. Despite many positive results, these countries have still failed to join the era of the technological revolution, which would allow them to correct their disadvantageous position in international trade, as well as to adequately develop and use human resources. Our paper focuses on the importance of regional cooperation in higher education and research for economic, social, and institutional development in the SEMCs. We demonstrate that universities in developing countries face greater challenges than their counterparts in the developed countries. We focus on assessing the European Union's (EU) efforts and contribution to the Euro-Mediterranean integration and institutional change since the future development of the Mediterranean countries is linked to the European integration processes. Finally, the paper outlines recent trends in the interconnection between regional integration in the EU and the Mediterranean. Our results might be of special interest for the policymakers and academics in the field of higher education and regional economics.