At a time when Russia is an economy based on the generation, dissemination and application of knowledge, dynamic economic growth, the level of competitiveness in the national and global level, the degree of national security have become defining achievements in science and technology. GDP growth and an increase in productivity in developed countries is mainly due to the production and sale of high technology products and services. Russia, despite the obvious advantages (technical and scientific potential, highly qualified personnel, a significant scientific base) is only in the initial stages of the transition to a new development paradigm that is due, above all, to the internal problems of the innovation environment. In order to implement the strategy of innovative development of Russia it is crucial to improve the quality of the work of national financial institutions and ensure the effectiveness of the trust money redistribution through the development of new financial arrangements. As world experience shows, one of the most effective methods of economic innovation is a public-private partnership (PPP) in the field of science and innovation. At present, public-private partnership is understood, as a rule, in two senses. In the theoretical context it is a system of relations between the State and business in contract form which is widely used as a tool for national, international, regional, city, municipal economic and social development and planning. From the practical point of view, it is specific projects implemented by various government bodies and business together or by private companies only at sites of the State and municipal property. Main directions of PPP in the innovation sphere are participation of the State in the development of venture capital financing; public-private financing of various programs, innovative orientation of the State order for research and development; public promotion of institutions of the modern market innovation, centers for technology transfer, patenting and protection of the rights of intellectual product owners. This PPP also relies on a rich international experience which must be claimed in Russia in connection with the unsatisfactory rate and extent of innovation in the economy.