The article is relevant as the fuel and energy complex (FEC) ensures work and activities of Russia as a whole and the consolidation of its regions, formation of a significant part of budget revenues and foundations of innovative economic development. The purpose of the study is to identify priority areas for the development of the fuel and energy sectors based on a comprehensive analysis of the development of their innovation and investment activities. Research methods include dynamic, coefficient and comparative analysis, which allowed us to identify trends in the development of the Russian energy sector in 2008-2017. It is noted that the need for large-scale modernization of the fuel and energy complex, which will require significant investments and support from state authorities. A comprehensive study of the State Programs of Russia was conducted - “Energy Efficiency and Energy Development”, “Development of the Nuclear Energy Industrial Complex”, and Corporate Innovation Development Programs (PIR).?The results of the study identify priorities for innovative development in the electricity, oil, gas and coal industries of the fuel and energy complex. The conclusions formulated will allow for a more effective innovation policy in the fuel and energy sector.