The study identifies the priority areas for implementing innovation and investment projects aimed at increasing management of a portfolio of such projects. The author describes a methodical approach for determining a functional structure of the portfolio management system of innovation and investment projects, which integrates various elements of the management system both horizontally and vertically. It is proved that introducing the portfolio management system makes it possible: to describe the strategy of an enterprise by determining the importance of goals and criteria for their achievement; to develop a portfolio of projects taking into account their strategic importance and cost effectiveness; to model a portfolio of projects taking into consideration the changing factors (for example, budgetary and resource constraints); to pay attention to the interconnections of the projects while creating a portfolio; to ensure effective management and monitoring of a portfolio of projects that illustrate the processes and provide necessary and sufficient information for decision-making; to improve the efficiency of decision-making and responsibility of major participants of investment processes. The author has developed a mechanism for creating the information management system for managing a portfolio of projects, including a set of normative documents as well as necessary funds and methods for management of innovation projects, which ensure the effective implementation of various projects of enterprises.