Integration of head-mounted virtual reality (VR) devices has been revolutionary in health professions education. In disaster preparedness training, VR simulation-based learning exposes health care professionals to the unique challenges of diverse scenarios, enhancing their adaptability. The aim of the study was to evaluate the effectiveness of a head-mounted VR tool for teaching basic radiation emergency medicine skills to medical students. The participants were 64 medical students (5th-year) who underwent a 3-hour training session in radiation emergency medicine that was conducted via head-mounted VR devices. Students scored their perceived emotion, performance, and self-efficacy at various time points in a self-reported online questionnaire. Comparison of survey responses before and after the session showed significant differences in terms of neutral emotion (P = 0.011), negative activating emotions (P < 0.001), and negative deactivating emotions (P = 0.004). The post-hoc test revealed statistically significant differences in negative activating emotions between before and during (P < 0.05), and between before and after (P < 0.05) the VR simulation. In addition, negative deactivation and neutral emotions changed significantly after the simulation. The use of head-mounted VR devices was effective in modulating medical students' emotions and contributed to improving their perceived performance in radiation emergency medicine.