The research aims to study the state of the use of information technologies in the higher education system of Kyrgyzstan. Within the research framework, the authors studied strategic plans and programs aimed at creating an information society in Kyrgyzstan. The authors described the problems that have arisen as a result of the impact of digital technologies on the education system. The authors obtained information on the development of computer technology in Kyrgyzstan since the late 1960s. The authors studied the documents adopted in the direction of informatization of education, as well as the nature of the proposals in the documents related to the development of the system of higher professional education using information technologies. Based on the analysis of the work and the practice of using information technology, the authors studied the areas of the use of information technology in universities. The existing problems in using information technologies at the university are also noted. Eliminating the identified problems makes it possible to improve the activities of universities related to training highly qualified personnel. Moreover, the authors identified promising directions for using information technologies in the higher education system. These directions primarily include the improvement of e-learning, the creation and use of the capabilities of intelligent systems and neural networks in improving the effectiveness of learning, and the development of the basic provisions of cybersecurity in education.