The article is devoted to the formation of programs for the development of Russian universities in accordance with the urgent tasks facing the Russian higher education. The development programs of the leading universities of the Russian Federation included in the "Project 5-100" program have been analyzed and the main projects implemented by these universities also have been identified and analyzed. On the basis of the collected data and the analysis which was carried out, recommendations were formulated for the universal part of development programs, including composition of the main projects. Approaches to program management based on project management tools have been formulated. They will allow to conduct a comprehensive modernization of all components of the university's activities. The approaches provide the economic viability and integrity of the development of the university.