The task of comprehensive development of the economy of rural and urban areas in the regions of Russia to create socio-economic conditions for development in order to reduce population migration, ensure sustainable development of the territory, a high level and quality of life of the local population - is currently one of the priorities for the Russian economy. The study of international experience has shown that the comprehensive development of territories must begin with the construction of infrastructure that allows creating conditions for a high-quality standard of living of citizens. Then it is necessary to form the sectoral structure of the economy of the territory, which should be as diversified as possible in order to stimulate high growth in the level of income of citizens. The article discusses the principles of developing programs for the comprehensive development of the economy of the territory, the size and sources of funding for such events at the federal and regional levels, as well as the stages of implementation of measures, the reasons for the emergence of risks and restrictions that are advisable to take into account when creating comprehensive development programs, the effects at various levels from their implementation. The results obtained can be used in the implementation of the spatial strategy of Russia, taking into account the territorial and sectoral specifics of regional development.