This study aimed to assess the public health impact and cost-effectiveness of gender-neutral vaccination (GNV) using a nonavalent vaccine (9vHPV) in Japan. We used a published, validated dynamic transmission model to estimate the cases of, deaths from, quality-adjusted life years (QALYs) lost to, and costs of diseases associated with HPV genotypes included in the 9vHPV vaccine. These outcomes were modeled over a 100-year time horizon under different GNV and female-only vaccination (FOV) strategies. The primary analysis compared GNV to FOV at a female vaccination coverage rate (VCR) of 30% and male VCR of 15%. Scenario analyses assessed the effects of varying these VCRs, the age at vaccination, and the discount rate. In the base case, GNV averted an additional 2,070 female and 1,773 male deaths from HPV-associated cancers compared to FOV and was cost effective, with an incremental cost-effectiveness ratio (ICER) of 4,798,537 ¥/QALY from the payer perspective (direct medical costs) and 4,248,586 ¥/QALY from the societal perspective (including costs of lost work productivity). The ICER of GNV versus FOV was higher in scenarios with higher VCRs. However, the ICER could be reduced compared to the base case by implementing vaccination at <15 years of age to reduce the number of vaccine doses required or by reducing the discount rate to assign greater value to the long-term cancer prevention benefits of HPV vaccination. This study may be limited by inaccuracies in the model's input data and assumptions, as well as the exclusion of some societal costs, which may have underestimated cost-effectiveness. Including boys and men in Japan's HPV vaccination strategy is predicted to provide additional public health benefits compared to FOV and to be cost effective, particularly while the female VCR remains low and if the full vaccine series is completed before age 15.