The authors set a goal - to show the role of the formation of entrepreneurial universities as one of the elements of a new innovative model for the development of the country's economy and to recommend solutions. Particular attention is paid to the relationship between the research in universities and achievements in agricultural sector, where the process of organizing a new type of university becomes necessary in connection with the current situation in the world and the republic associated with the pandemic. Higher education institutions characterized by research and entrepreneurial activities are created according to the triple helix model and are thriving in the United States, Great Britain, Australia and many other countries. It is noted that scientific developments in the field of agriculture do not always meet the requirements of consumers. Often they are not known in the educational system or may be non-competitive, not comparable to the demands of practice. Due to the seasonality of production and instability of income, agricultural enterprises are not able to finance the costs of mastering and introducing innovative technologies into production. The dynamics of development of agricultural sector (gross agricultural output, yield per hectare for the main types of crops, livestock population), the quality of educ national programs for agricultural specialties are shown. The costs of financing science in Kazakhstan are considered on the basis of ratings of the national chamber of entrepreneurs "Atameken". Entrepreneurial universities have real opportunities to solve the problems of harmonizing relations between universities and agribusiness, contribute to improving the image of both parties, increasing their investment attractiveness and competitiveness in market environment.