The aim of this study is to identify problems and identify options to improve current approaches to securing financial resources of innovation activities of enterprises. The study used the methods of systematic and comparative analysis. According to the results of the study proposed a scheme of funding sources and forms of innovation in enterprises. The novelty of the scheme is presented in a comprehensive approach, which shows the sources of funding for innovation activities by type of property ownership levels, relative to the property, as well as forms of financing innovative enterprises. In addition, on the basis of the study authors proposed an algorithm of financing innovative enterprises, based on debt issuance. The developed algorithm allows the use of innovative financing in the process of the most important sources of funds from various fields and thus solve the problem of resource support for innovation. The novelty of this algorithm is a sequential process involving the investment of various categories of potential investors for the financing of innovative companies in the Russian Federation. The proposed financial instruments aimed at stimulating innovation in enterprises.