Models, methods and mechanisms of project-oriented management of universities are the subject of the research. Formation of the balanced scorecard in project-oriented management of universities is the purpose of the work. There are the following research objectives: analysis of strategic development projects of higher education institutions, defining the mission of universities in carrying out the educational and scientific projects, forming a model of challenges, opportunities, threats and prospects in implementing the university mission, developing a conceptual model of project-oriented management of universities based on the implementation of the Key Performance Indicators system. The following methods such as project management methods, project portfolios and programs, theory of systems, tools of the optimization modeling are used. There were obtained the following results. Considering the dynamics of development universities that have introduced a project-oriented management system, it was found that the use of the project approach improves the efficiency of universities. It was found that the basis of this approach is the development Strategy of the university. The mission of the Odesa National Maritime University is defined, which consists in training specialists competitive on the world labor market in a certain field by involving leading research and teaching workers, using the results obtained in research projects and implementing innovative teaching methods. It was found that in the current situation in higher education, the task of implementing a project-oriented model of higher education management is solved by introducing a balanced scorecard, i.e. Key Performance Indicators. The model of formation the higher education institution project portfolio is developed taking into account available resources on the basis of introduction of the balanced scorecard. A conceptual model of project-oriented management of the Odesa National Maritime University has been developed, which will allow monitoring and adjustment of university performance target indicators during the implementation of the strategic plan for the university development.