The development of agriculture in the Kyrgyz Republic requires a shift toward an innovation-driven model that ensures production sustainability and food security amid regional disparities, climate challenges, and limited resources. In the context of globalization and the digital transformation of the economy, the integration of innovations aimed at improving the efficiency of land, water, and labor resource use becomes especially important. Differences in technological capacity, infrastructural support, and investment opportunities underscore the need for a region- and sector-specific approach to managing innovation processes. The research aims to substantiate the organizational, economic, and methodological foundations of innovative development in the agrarian sector, considering the country’s natural-climatic and socio-economic characteristics. The methodological basis includes systemic, institutional, and reproductive approaches, as well as comparative, structural-dynamic, and factor analysis. Based on the assessment of innovation potential and constraints, the authors identified the key determinants of development, which are technological readiness, infrastructure accessibility, human capital capacity, and the quality of the institutional environment. The outcome of the research is a hierarchical model of priorities for the innovative development of agriculture, focused on building a competitive production system capable of ensuring sustainable economic growth, food security, and the social well-being of rural areas. The findings may be used in the development of national and regional strategies for modernizing agriculture.