To achieve a long-term stable growth in the social and economic well-being of the region, it is important to pay attention to the level of education in the latter, since the indicators that determine the level of higher education in the region and the indicators of the region’s competitiveness are interdependent. The authors’ aim is to work out a unified methodology that would make it possible to compare the level of development of any Russian region with the level of education in it. This research paper, based on the use of comparison methods, statistical grouping and matrix modeling, proposes a methodology for clustering regions according to the level of higher education development and the competitiveness of the territory’s economy. By means of the analysis of statistical information presented in the official databases of Rosstat and the Ministry of Education and Science of the Russian Federation for 2021, the study identifies trends describing the correlation between the level of development of regional higher education and gross regional product. This paper is the first to provide a detailed analysis of the ratio of the regional higher education development index (based on seven groups of indicators: level of education, higher education personnel sufficiency, development of scientific potential in higher education, solution of social problems in the region, reputation of the regional higher school, development of the digital economy, infrastructure) and the gross regional product of 85 Russian Federation members divided into federal districts. The authors classify regions into clusters according to the level of higher education development in the region and the level of GRP. This clusterization allows them to formulate assumptions and conclusions regarding the reasons for the regions’ belonging to a specific cluster, as well as to discuss possible strategies for the development of higher education.