A specialist in the field of transport systems must have high educational and professional independence, in the process of his future professional activity, constantly develop his competencies and master new ones. In particular, he needs to possess developed research skills, to be ready to solve new problems constantly arising in transport. The article proposes the author’s approach to the formation of educational and professional independence of future transport specialists, aimed at the development of research skills. Based on the competence-activity approach, the authors propose a system of work on the formation of a research component in the competences of a future transport specialist as part of the formation of his educational and professional independence. The materials of the article contain a description of the pedagogical experiment and the results of the pedagogical experiment on introducing the proposed ideas into the educational process of the railway university. The study was carried out on the basis of the Federal State Budgetary Educational Institution of Higher Education “Irkutsk State University of Railways”.