One of the directions of state management of personnel training within the framework of the national higher school is the development of a number of educational projects. The Project 5–100 is aimed at ensuring the global competitiveness of leading Russian universities – their entry into the authoritative world university rankings. Decisions taken within the framework of public administration, although aimed at achieving the goals of the Project, are not always accompanied by the expected positive results. It is proposed to describe the uncertain possibility of negative consequences of the adoption and implementation of a specific management decision through the risk of state management of this Project. In view of the fact that the consequences of the implementation of these risks carry the threat of destruction of the Russian higher education system itself, they must be considered as systemic. The high significance of the Project for the entire Russian higher school determined the need to identify systemic risks of public administration primarily at the federal level. To identify a particular systemic risk, the authors have developed a special procedure. The analysis showed that the implementation of most of the risks of managing on this Project did not allow achieving the goals set for it, that negatively affected the development of the entire system of Russian higher education.