Effective management of project portfolios at science-based enterprises, which are now challenged by a dynamic turbulent environment, requires a continuous integrating activity. The goal of the latter is to maximize the return on implementation of the entire set of projects, bearing uncertainties and losses in mind. Thus, the article covers latest research in and approaches to project portfolio management. The methods and mechanisms of project portfolio management are analyzed, the weaknesses of project portfolios are detected; major issues and factors influencing their management are identified as well. The functional model of the value-oriented anti-risk science-based project portfolio management using the functional modeling methodology of IDEF0 are constructed. It takes into account the basic value indicators of the projects and portfolios that meet specified requirements, minimizes losses and uncertainties, and provides the maximum integrated value of project portfolios.