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The relevance of the research is determined by the need to update the management structure of scientific projects within higher educational institutions in accordance with modern economic realities and internationally recognized standards, the essence of which is the transition from a rigid hierarchical management system and orientation towards the commercialization of the results of scientific and technological activities. Therefore, the purpose of this scientific article is to develop a functional model for scientific project management within higher education, the components of which, unlike existing models, will be characterized by a project-oriented direction. To achieve a certain research goal, general scientific research methods were used, including analysis, synthesis, generalization, comparison, systematization, modeling, as well as structural and mathematical methods, taking into account the key principles of structural-functional and system approaches. The article analyzes a number of scientific works of Ukrainian and foreign scientists on the topic of methodological substantiation of the specifics of management of research projects in higher educational institutions. The key concerns of the current state of scientific project management within the Ukrainian scientific space have been identified, in particular, the rigid organizational and staff management structure with the predominant role of the top management, insufficient financial support of scientific and technical activities, as well as limited access to the results of scientific and technical activities. The author’s economic and mathematical model of scientific project management in higher education institutions has been developed considering functional indicators. It is proposed to introduce a body for commercialization of the results of scientific and technical activities, which will help optimize the financial support of scientific and technical activities. The necessity of developing international cooperation within the framework of scientific and technical activities and the organization of scientific projects in particular is substantiated. The practical value of scientific work lies in the development of the author’s own methodological support for the proper functioning of scientific project management with the prospect of its further application in practice