Background: During the mumps outbreak in Japan in 2016, 159,031 cases were reported. In a survey conducted in 2015, mumps vaccination rates for the first dose were 30%–40%. However, the rates for two or more doses were not determined. We assessed the mumps vaccination rates and mumps infection prevalence according to vaccine doses received. Design and methods: This was a multicenter cross-sectional study. Students from three universities participated in 2019. Informed consent was obtained from the students and their guardians. The primary outcome was the prevalence of breakthrough mumps infection according to the number of doses of vaccine received. We collected data on past illnesses of vaccine-preventable diseases and vaccination history using a questionnaire, photocopies of the Maternal and Child Health Handbook from the guardians, and virus antibody titers from the universities’ health centers. Results: This study assessed 2004 eligible students and included 593 (29.6%); of these, 250 (42.7%) had a mumps infection history. Furthermore, 264 (44.6%), 31 (5.2%), and 2 (0.3%) students received the first, second, and third doses of mumps vaccine, respectively. The mumps seropositivity prevalence was 43.2% ( n = 127), 36.7% ( n = 97), 26.7% ( n = 8), and 100% ( n = 2) for the no-, first-, second-, and third-dose groups, respectively ( p for trend = 0.09). The mumps infection prevalence rates were 69.8% ( n = 203), 11.3% ( n = 28), 3.9% ( n = 1), and 0% for the no-, first-, second-, and third-dose groups, respectively. Conclusions: Approximately 1 in 10 students who had received only one dose of mumps-containing vaccine had a breakthrough infection history.