The purpose of the article is to study the system for assessing the quality of education in the context of risk management in the activities of higher educational institutions. The definition of the concept of «risk in the higher education system» is given. The methodological basis of the study is the provisions of the theory of system analysis, the concept of process management and management by results; provisions on the social, activity, creative essence of the individual and the multifactorial nature of the development of the effectiveness of his management process and the justification of its criteria and indicators; system-structural approach, its application in the theory and practice of pedagogical science; approach to action, quality management of education, methodology of pedagogical research. The article covers the analysis of the research of domestic and foreign scientists in the field of strategic management and quality assurance in higher education institutions, the use of risk management, the analysis of the processes of activity of higher educational institutions. The authors propose a methodology for identifying and managing risks at the university. To prevent risks, it is recommended to develop a risk management map, which is determined by the importance of risks and the likelihood of their occurrence. The authors studied risk categories, as well as assessing the degree of risk. Risk assessment provides constructive information and analysis to consider specific risks and make informed decisions about the choice between options. The authors also outlined recommendations to reduce the occurrence of risks in the process of activity of the Kazakh agrotechnical research university named after Saken Seifullin. The use of the above elements allows us to develop not only the organization of the educational process in higher educational institutions, but also its quality management system.