In the era of the knowledge-based economy, countries and regions that provide the fastest innovative development benefit from the global competition. Direct implementation of innovation policy is carried out by specific enterprises, in which innovative development plays the role of a key factor in the toughening competition. Thanks to state efforts, the basis of national innovation system has been formed. In particular, there are some federal and national research universities that provide research, innovation, and staffing for high-tech industries, and Russian venture funds, technology parks, industrial and agricultural and industrial parks, and business incubators. The Skolkovo Innovation Center has become widely known. Special attention is paid to region innovative development with innovative infrastructure. The effective use of resource potential of the region involves strengthening and expanding economic ties, increasing the intensity of investment processes at all levels of social and economic system, developing the infrastructure base and increasing the role of innovation in the system of economic interests of the region. The article discusses the key aspects of state and bank financing of innovation, not only at the federal level, but also at the regional level. The paper presents the complexity analysis of financing innovations associated with limited budgetary opportunities, insufficient participation of banks in the implementation of innovative investment projects. There are ways of problem solution to invest innovative activities of economic entities.