Relevance. This study investigates the relevant issue of training specialists with knowledge and ability to apply information technologies in professional activities. The relevance of this study is conditioned upon the national programmes and regulatory documents adopted in recent years in the field of education and the importance of being capable of using and studying computer science in modern times. Purpose. The purpose of this study lies in developing a methodological system for teaching students in a competency-based approach, which would maximise the impact on the quality of education and the level of proficiency in computer science. Methodology. The following general scientific methods were used in this study: logical-historical, pedagogical observation, analysis, synthesis, systematisation and generalisation, methods of mathematical statistics, as well as the Help&Manual programme. The use of the created methodological system was carried out involving students of Nasirdin Isanov Kyrgyz State University of Construction, Transport and Architecture, Kazakh University of Transport Communications, Almaty University of Power Engineering and Telecommunications named after Gumarbek Daukeyev in 2018-2019. Results. The result of this study is the motivation-target, content, activity-based, and evaluative-reflexive components of the methodological system highlighted by the authors, each of which is characterised quite succinctly and accessibly. The authors of this study covered the role of the course of computer science in the development of students’ skills in using the possibilities of information technology in the professional sphere, the development of instrumental competencies. Conclusions. During the study, a model of the methodological system of teaching students was created, which was based on factors, conditions, principles, and criteria of methodology, competencies, and the level of their development, forms and methods of teaching. The results obtained can be used in the methodological work of university teachers and in advanced training courses for schoolteachers.