The purpose of the study is to design a training programme for master’s students of the engineering specialisation pursuing a degree in bioengineering, based on the principles of transprofessionalism and social partnership. The paper presents the content, methodological foundations and educational technologies that make it possible to form specialisation competencies in the field of nuclear medicine in future graduates in a specially organised practice-oriented educational environment of a university by integrating production into the educational process. Scientific novelty lies in developing a concept and constructing a model for an educational programme specialisation in the subject area of nuclear medicine within the master’s programme in “Biotechnical Systems and Technologies”. As a result, it has been shown that the developed educational programme specialisation “Nuclear Medicine Technology” as a system is determined by means of mastering several training modules interconnected on the basis of a transdisciplinary approach, which contributes to the development of students’ innovation skills. The successful trial of the programme, which has been taking place in the real educational process for five years since 2017, has led to the creation of a scientific and educational cluster in the structure of a federal university, where a key role in training is assigned to students’ interdisciplinary projects that are carried out at the graduate department together with the Cyclotron Center for Nuclear Medicine of the Ural Federal University.