Higher education plays an important role in promoting the concept of sustainable development and achieving the 2030 UN goals. In modern society, higher education institutions act as educational and research centers and impact the economy, politics, and social sphere of the region. At the same time, unlike the world's leading universities, Russian higher education institutions demonstrate a predominantly low level of involvement in the implementation of sustainable development. In this regard, the assessment of regional universities for sustainable development becomes relevant. Scientific novelty lies in the development of a system of assessment indicators and methods for the regional system of higher education for sustainable development. The methodology evaluates five functions of the higher education system by twenty-four indicators. An information base serves to be available statistical data for six years (2015–2020). The methodology is tested with the Volga Federal District regions. The study revealed that the higher education system in the Republic of Tatarstan achieves the highest level in its performance, while the higher education system in Kirov region and Udmurt Republic shows the lowest level. Perm Krai demonstrates an interfunctional imbalance and an insufficient level of development of the higher education system for the region’s sustainable development. Correlation analysis detected a statistically significant relationship between the performance of the higher education system in the region and its sustainable development. The article will be of interest to researchers of sustainable development problems of territories, students and graduate students examining this topic; state and municipal employees involved in the implementation of the region’s sustainable development.