Universal attention to the higher education system transforms and complicates its processes. A variety of works around higher education try to study and solve a wide range of problems. Most of researchers pay attention primarily to the university as an independent unit, shifting the focus to the individualization and autonomy of universities. However, in the social sphere, leaving the university market or increasing the gap is a critical moment for interested parties, while the practice of combining several universities in order to increase their competitiveness, «saving» weak HEIs is a time-consuming and difficult process. Universities are units of the general system of higher education, which is characterized by endogenous and exogenous processes. The authors of this paper present methodological tools for assessing regional higher education systems based on the indicative method of analysis. These tools make it possible to draw conclusions on the (non-)uniformity of the system development and on its level, which is determined through the specified threshold values. The results of the analysis show that for certain blocks of the methodology, the gap between regional systems is increasing. At the same time, the leaders of the system are growing at a slower pace throughout the analyzed period, but they have firmly consolidated their positions. The catching-up systems are changing their positions, but a more active growth of indicators together with their low values does not allow these systems to overcome the average mark.Several other important conclusions are drawn. The existing infrastructure indicators do not meet the modern challenges of higher education, whose activities are increasingly integrated with research, whose infrastructure is assessed not only by the availability of fixed assets and the availability of space, but also by their use, generation of their own infrastructure and its commercialization. The more universities participating in the programs are concentrated in the region, the higher are the indicators of the system. Moreover, there has been revealed a positive dependence between the scale of the regional higher education system and its level of competitiveness.Our study also allows to draw a conclusion about the development of regional higher education systems both within themselves and relatively to each other. Positioning the region as demonstrating strong scientific and educational activities contributes to attracting resources (intellectual, human, financial), and vice versa. Therefore, it is necessary to develop (preventive) measures to stimulate the system.