The transformations that are currently taking place in the world economic system are forcing scientists to research the factors that allow national economic systems to be sustainable and competitive in today's realities. The key direction for Ukraine with its fertile black soil is the innovative development of the economy as a whole and enterprises, especially agricultural, in particular. The article analyzes the innovative development of enterprises in Ukraine, the quantitative indicators of recent years in terms of innovative development and financing and investment in innovative development of enterprises. It is suggested to consider agricultural enterprises an economic system to explore in more detail their innovative development, the factors that influence it, the methods of its improvement, and more. The specific features of agricultural enterprises as an economic system are emphasized, in particular, their strategic role in terms of food security, their key importance for rural areas and rural population. There are two main directions of innovative development of agricultural enterprises: improvement of production technologies and improvement of quality of labor resources. The importance of labor resources for the effects of the functioning of agricultural enterprises is emphasized. The authors of the article have proposed a methodological approach to material incentives for the staff at agricultural enterprises and adapted it to a specific agricultural enterprise.