The article considers the system of internal control as the main element of the organization of a competitive, promising university. Universities are on the path of modernization, adaptation of their activities for the effective implementation of this process, universities need to productively evaluate the internal control system. To form an evidence base on the need to revise the role of the internal control system, two studies were conducted, namely, one was aimed at studying methods for assessing the internal control system, the other proved the effectiveness of the assessment using modern methods, as it included an example of assessing the internal control system. In the theoretical part of the work, an analysis was made of the interpretation of the term “Internal control system” in order to form a clearer understanding of the issue. In the practical part, an analysis was made of qualitative, quantitative and related methods for assessing the internal control system. Based on this study, trends, conclusions regarding the effectiveness, potential, reliability of the considered methods, the possibility of their joint work were determined, and recommendations were formed on possible assessments of the internal control system. The final part of the analysis was an example of assessing the effectiveness of the internal control system, the object of the study was the Federal State Autonomous Educational Institution of Higher Education “UrFU named after the first President of Russia B.N. Yeltsin, as one of the largest universities in the Russian Federation.