The Eurasian Economic Union is a major integration project nowadays, but various problems arise in its implementation course, including in the economic field and the humanitarian cooperation sphere, which determines the relevance of the research. The paper focuses on identifying these problems and finding promising directions for the long-term development of the EAEU. The problems of the EAEU that hinder its effective development are analyzed with the use of classical scientific knowledge methods (analysis, deduction, and induction). The scientific novelty of the research is in the development of the author’s proposals for creating conditions for sustainable science and education interaction. It is the one that can provide a solution to the key task of the EAEU, its innovative production and competitiveness modernization on the world market. © Springer Nature Switzerland AG 2020.