The paper is devoted to the study of urgent problems of innovation activity stimulation on the example of agricultural universities as an important condition for the improvement of the efficiency of the agro-industrial complex and the development of the agricultural industry in general. The ambitious tasks for a significant increase in labor productivity in the agricultural sector, as well as the creation of high-tech jobs are impossible without proper staffing and scientific support. The effective import substitution and maintaining food independence is impossible without the introduction of new technologies, a significant increase in labor productivity in agriculture and the increase in the attractiveness of rural life. These challenges and priorities set the agenda for the formation of requirements for the system of agricultural education and new competencies of youth and teachers. In this regard, the problem of innovative activity of agricultural universities is being updated not only as a source of highly qualified personnel for agriculture, but also as centers for the development of innovations in this area. In paper, it is shown that systemic problems in the field of education are organically linked with the transformations of university science in the second half of the 20th century, when the basic principles and approaches to the organization of scientific research in universities were laid down. It is pointed out that despite numerous attempts to intensify science in agricultural universities, there are a number of constraining factors that affect their potential in the development of innovations in the agricultural sector.