In the modern realities of the global change in the technological order and the emergence of a post-industrial society, innovative activity strengthens its significance as the most important resource for socio-economic development. Territorial differences in the potential for innovative development, which impede the effective integration of the northern regions into a single innovation system of the country, predetermine the need for a deep study of the problems of their development and the study of the main factors and prospects in the field of innovation. The study focuses on the northern regions of the European part of Russia, since they concentrate more than half of the human potential of the North and determine the strategic prospects for the development and strengthening of national security in the Arctic zone of the Russian Federation in the face of existing risks and challenges: environmental, social, economic and geopolitical. The purpose of this work is to identify prospects and to assess the current state of innovative development of the northern regions of the European part of Russia. In order to achieve the goal, the methods of statistical and comparative analysis, the dialectical method were used. The informational basis of the study was made up of data from Rosstat and the departmental civil service at the regional level. The analysis demonstrates the differentiation of the regions of the northern European part of Russia at the level of innovation and regional economic systems that include it. The most important prospect of overcoming the weaknesses of regional innovation systems is their integration and mutual complementarity, which is sometimes achievable with new systemic tools for the spatial organization of the economy, in particular, the special economic regime of the Arctic zone of Russia. The study was conducted on the example of five regions of the European North of Russia: the Arkhangelsk Oblast, the Murmansk Oblast, the Republic of Karelia, the Komi Republic and the Nenets Autonomous Okrug.