A regional model of sustainable development in rural areas is proposed as a result of its institutional design. The cyclical management process is implemented through strategic planning, forecasting and resource provision of positive transformations of a socio-economic nature. The purpose of the study is to develop the organizational and managerial system for ensuring the basic parameters of sustainable rural development in the aspect of constructing favorable institutional conditions for management and residence. The study is based on the municipal formation of Leningradsky district (Krasnodar Krai, Russia), the administrative composition of which is represented exclusively by rural settlements. The methodological approach involves modeling the local structure of regulation of socio-economic relations for improving the institutional environment of rural areas. In addition, the economic and statistical analysis of the current state of studied areas covers quantitative and qualitative indicators. Based on the structural and functional analysis of management systems, comparison of general and specific indicators, evolutionary consideration, interdisciplinary synthesis, conclusions are formulated about the prospective state of the organizational and management system. The scientific novelty of the study lies in the substantiation of an innovative mechanism for stimulating sustainable development of rural areas through expanded reproduction and implementation of human capital. The solution of infrastructure problems, a significant increase in the cost of labor resources and the production of other positive changes are associated with the improvement of program-targeted management, the growth of entrepreneurial activity and the transition to living standards for rural citizens, implemented according to the agropolis type.