The application of the transdisciplinary approach in high education is one of the most important ways to improve the quality and fundamental training of students in technical universities, especially for master’s programs. Transdisciplinarity is a deeper and more transparent level of integration of various professionally focused basic disciplines. In contrast to interdisciplinary training transdisciplinarity allows masters to form the necessary skills for self-improvement and self-realization during choosing their own career path. The educational program “Biomedical engineering” based on the UrFU internal educational standard for the training direction 12.04.04 (“Biotechnical systems and technologies”) is scientifically justified and designed on the principles of transdisciplinarity. The educational program ensures the training of highly qualified personnel in biomedical engineering which aimed at mastering the methods of related sciences and met the needs of modern production.