The issue of the coordination between different levels of power in the governance of higher education is crucial for countries with high levels of regional heterogeneity. This paper analyzes the features of transformation of national-regional relationships in higher education in Russia based on the framework of governance and management in higher education systems. Analysis of “higher education federalism” shows that the current highly-centralized governance model in Russian higher education is the result of a chaotic transformation process after the collapse of the Soviet Union. Also paper explains that actual coordination between national and regional levels is insufficient for real participation of universities in regional social and economic development.