BackgroundVaccine administration skills are very important for physicians, especially in the era of global pandemics. However, medical students have reported that practical sessions to develop these skills are insufficient. Therefore, the aim of our study was to develop a vaccination training course for medical students. We also examined its educational effectiveness.Methods5th- and 6th-year medical students at the University of Tokyo were recruited to attend the vaccine administration training course in 2021. These students were our study participants. Our course consisted of an orientation part, which included a lecture on the indications, adverse events, and vaccination techniques of flu vaccines and practice on a simulator, and a main part in which the staff of the University of Tokyo Hospital were actually vaccinated. Before and after the main part of the course, study participants completed an online questionnaire that assessed their confidence in vaccine administration technique through a five-point Likert scale. We also surveyed their feedback about the course content and process. At the beginning and end of the main part, their technical competence in vaccination was assessed by two independent doctors. These doctors used a validated checklist scale (ranging from 16 to 80) and a global rating scale (ranging from 0 to 10). We used their mean scores for analysis. The quantitative data were analyzed through the Wilcoxon signed-rank test. For the qualitative data of the questionnaire, thematic analysis was conducted.ResultsAll 48 course participants participated in our study. Participants’ confidence in vaccination technique (Z= -5.244, p < 0.05) and vaccination skill significantly improved (checklist rating:Z= -5.852, p < 0.05; global rating:Z= -5.868, p < 0.05). All participants rated the course as, “overall educational.” Our thematic analysis identified four emerging themes: interest in medical procedures, efficacy of supervision and feedback, efficacy of “near-peer” learning, and very instructive course.ConclusionsIn our study, we developed a vaccine administration course for medical students, assessed their vaccination techniques and confidence in those techniques, and investigated their perceptions of the course. Students’ vaccination skills and confidence improved significantly after the course, and they positively evaluated the course based on a variety of factors. Our course will be effective in educating medical students about vaccination techniques.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12909-023-04299-w.