The article describes an integrated approach to the formation of the management system for the scientific and educational potential of a university as a dynamically developing phenomenon consisting of a set of closely interconnected components. The authors reveal the generalized structure of the potential, as well as the structure of its parts, which consist of interacting elements. The paper shows that there is a close relationship between the level of the scientific and educational potential of a university and the level of its innovative activity. We came to the conclusion that the formation of the effective management system of the scientific and educational potential of a university should be based on the level and dynamics of the innovative activity of its structural elements. With the involvement of the authors’ methodological tools, an assessment of the innovative activity of the universities of Ekaterinburg over the period 2013-2016 was conducted. In total, we studied thirteen universities including public and private institutions of higher education. On the basis of the conducted analysis, we substantiate the use of several management models in building a management system for the scientific and educational potential of a university. The result of this study indicates that each of the analyzed management models with their strengths and weaknesses contributes only to a partial implementation of the accumulated scientific and educational potential. Therefore, the management system of scientific and educational potential should be based on their effective combination. In the study, we used the data of both the Ministry of Education and Science of the Russian Federation and the Federal State Statistics Service. We also applied the results of innovation activities of higher education, presented on the websites of Russian universities, as well as the theoretical and practical results of domestic and foreign authors. The results of the research may be used in further studies related to the search of the directions for the development of the most effective management systems of the scientific and educational potential of a university, contributing to its revealing and implementation.