Japan recently approved a quadrivalent human papillomavirus (HPV) vaccine for males, but the 9-valent vaccine has only been approved for females. Given the low female vaccination rate due to concerns about adverse events in Japan, quantifying the risks and benefits of the HPV vaccination for males may help in deciding whether to vaccinate adolescent boys in Japan. Using quality-adjusted life years, the risk–benefit ratio for an adolescent boy receiving the 9-valent HPV vaccination was calculated. The male HPV vaccination reduced the QALYs gained due to head and neck cancer, anal cancer, penile cancer, genital warts, and recurrent respiratory papillomatosis by 401.63, 20.38, 9.40, 28.79, and 69.13 per 100,000 vaccinated persons, respectively. The total risk of vaccination was 11.85. The risk–benefit ratio for a 12-year-old boy who received the HPV vaccination series was found to be 0.022 (benefit–risk ratio, 44.670). In the sensitivity analysis, the risk–benefit ratio ranged from 0.0001 to 0.11 for all scenarios. Hence, much larger benefits than risks linked with the male HPV vaccination were observed from an individual perspective. The results support the inclusion of sex-neutral HPV vaccinations into the national immunization program as well as strengthens the decision for adolescent boys to receive the vaccination.