The current task of higher professional education is to train highly qualified specialists with a sufficient set of competencies that will allow them not only to master their profession, but also to fulfil their potential in related areas while solving real problems in priority guidelines of the Russian economy. Innovative development of education involves the integration of universities with research centers and industrial enterprises and requires new educational programs. The aim of the work is to develop the concept of designing the "Biomedical Engineering" educational program, implemented at the Ural Federal University in accordance with the requirements of the independently established educational standard for graduates in engineering. The principles making up the methodology of the program designing: scientific, systematic, practice-oriented, interdisciplinary approaches, convergence of sciences, as well as the introduction of high-tech information and communication technologies and transdisciplinarity of professional activity are detailed in the article. The presented model of the program forms universal, general professional and special professional competencies required in accordance with the direction of training. During the testing high efficiency of the educational program “Biomedical engineering” and its compliance with the requirements of the current economy were revealed with the help of the criteria of effectiveness, relevance and satisfaction of graduates with the program. The described approach to the designing of training programs for graduates in engineering allows us to prepare a holistically formed, competitive specialist with indepth knowledge within the profession acquired and ready to master new competencies in related fields. Such a versatile specialist meets the requirements of modern dynamic economy and is in demand in the labor market.