The urgency of the issue discussed in this article is caused by the need for development and assessment of new models and mechanisms of management of higher education institutions, which are connected with the development of the system of management of innovation projects and contribute to the development of educational institutions. The aim of the article is to give a theoretical justification and assessment of the system of innovation project management at a higher education institution as well as to assess its efficiency. The leading research methods are pedagogical modeling and project planning, theoretical analysis and compilation of the educational practice in innovation project management, and mathematical methods of statistics which help to make a comprehensive analysis of efficiency of the system of innovation project management. The article reveals the role of the system of innovation project management at a higher education institution as a complex of methodological approaches, principles, and mechanisms which provide for successful implementation of innovations in scientific, international, economic and other activities of an educational institution. The article also describes the peculiarities of innovation project management connected with the specific character of management entities, subjects to management, management processes. Efficiency of the model of development of the system of innovation project management is justified.