Research facilities such as spallation sources and synchrotrons generate radiation for use in atomic-level or molecular-scale experiments. These facilities can be viewed as complex safety-critical systems. An important aspect of the safety management of such systems is the short safety education and training programme the users are required to undergo in order to gain facility access. As research on the topic is limited, this study aimed to increase the knowledge about current education design and practice using the perspectives of safety science and pedagogy. Study objectives were to identify preconditions that impact the safety education design, to describe current design and practice of the safety education, and to identify weaknesses and possibilities for improvement. Site visits with a total of 20 interviews were performed at three research facilities. The results show the need for sufficient resources to maintain learning activities for users, provide pedagogical continuing education for educators, and maintain safety culture-enhancing activities to meet the challenges of having large numbers of short-term facility users. Increased focus should be placed on safety-related competence needs and the mapping of these to match the competence of individual users. New thinking and innovation can benefit the design and provision of such education activities, based on both socio-technical system and system safety perspectives.