This article discusses the experience of the transformation of the University of Tokyo to an entrepreneurial university in the context of the institutional approach and B. Clark’s concept of entrepreneurial university. It vividly shows the dependency of the current University’s development trajectory on the historical retrospective of decisions made by the University’s administrators. The key elements of an entrepreneurial university were studied – a strengthened steering core, an expanded developmental periphery, stimulated academic heartland, a diversified funding base, as well as an integrated entrepreneurial culture of the university. The directions of using the described experience for Russian universities, in particular, for Lomonosov Moscow State University, are suggested.