The problem of choosing a strategy for the development of depressed regions is of particular importance both from the point of view of ensuring economic security and improving the dynamics of the national economy. At the same time, most regions trapped in depressiveness during the period of market reforms, cannot reach the trajectory of sustainable economic growth. One of the reasons for this situation is the underestimation of the importance of the innovative strategy. The purpose of the work is to develop methodological aspects of the formation of an innovative strategy and the justification of effective tools for its implementation. The official statistics of Rosstat, as well as the strategies of socio-economic development of the regions of the North-Western Federal District are used as the information base of the study. The research methodology is based on the systematization of effective tools to support the economy of depressed regions, presented in the scientific literature, as well as the analysis of the regional practice. The paper systematizes the principles of strategy formation, the priority of human capital development is among the most important, as well as the need for an ecosystem approach that ensures effective interaction of all participants in the innovation process. The systematization of regional practice made it possible to identify the declaration of innovative strategy in the strategic documents of depressed regions. Thus, the importance of integration tools that make it possible to use external resources and compensate for the problem of insufficient own scientific and technical potential is underestimated. The results of the study contribute to the development of strategic planning methodology at the regional level.