The purpose of this article is to develop a theoretical mechanism for planning free cash flows of an innovative project, provided that it is necessary to ensure a highly probable possibility of its implementation. The review of special literature shows that the problem of resource risk management of investment projects in the world economic practice is not new, but the methodological apparatus of project risk management is not sufficiently developed. The result of applying the method of induction in the analysis of the General theory of project risk management terms the planned commercialization of innovation, identified areas of possible application of effort in the management of project risks in investment planning implementation of innovations, the main of which is recognized as a building of special reserve funds within the project budget for the relief of consequences of the possible manifestations related risks. Alternative methods for justifying the values of risk reserve funds for cash flows from operating activities and capital expenditures were created by means of an essential analysis and an actual methodology for constructing the values of risk reserve funds. Using classical deduction to previously obtained results, an algorithm for planning free cash flows of an innovative project was developed and formalized, provided that it is necessary to ensure a highly probable possibility of its implementation. The algorithm for accounting for project risks has been tested on practical material. The results of the study are not only of theoretical and methodological significance, but also have a high practical significance. The scope of their application is not limited to the use of high - tech innovations in the framework of investment design. They can and should be used in all cases when it is necessary to reliably achieve the priority goals set by the initiators of risky investments in the real sector of the economy in the future.