The article discusses theoretical and methodological approaches to the formation and development of an innovative agricultural system. Based on the analysis of theories of innovations, the authors clarify the essence of innovations and innovative systems, prove the need for a transition to innovative systems, taking into account current global trends and internal contradictions in the economic environment. The features of the process of formation of an innovative agricultural system as a result of transformation of the agro-industrial complex in the context of? transition to an export-oriented economy are disclosed. A methodology based on an assessment of the institutional component of an innovative agricultural system is proposed. Based on the analysis of innovative development indicators, the influence of the level of the institutional component on the innovative activity of agricultural organizations in Russia is proved. The authors reveal the reasons for the low innovation activity in the agricultural sector and, on this basis, propose a system of measures and tools aimed at supporting and stimulating innovation in the agricultural sector.