The relevance of the study is to consider the specific features of innovation management from the point of view of the project approach. The theoretical and methodological basis of the study was the works of Russian and foreign researchers in the field of management theory, project management, portfolio management, innovation management, project governance. The authors used analysis and generalization of domestic and foreign theory and practice, as well as the method of "Case study", in the framework of the case: strategic portfolio analysis (BCG matrix), interviewing, questioning, investment analysis as research methods. Analysis of existing approaches to the formation of a portfolio management system of R&D projects showed a low level of elaboration of the issue. The article presents the results of testing the project of development of the portfolio management system of projects and programs in the field of research and development work, taking into account the identified features on the example of a high-tech enterprise.The expediency of implementation of project management methodology and formation of R&D project portfolio management system as a tool to improve the efficiency of investment activities, the implementation of strategic goals and improvement of the competitiveness of the modern company are confirmed.Keywords: project management system, R&D, innovation projects portfolio.