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Human papillomavirus (HPV) can cause several diseases, including cancers, in both sexes. In January 2020, the Hong Kong government launched a school-based vaccination program for girls 10-12 years of age with the 9-valent HPV (9vHPV) vaccine for the prevention of HPV-related diseases; however, boys were not included. The current study estimated the potential health and economic impact of a routine gender-neutral vaccination (GNV) approach compared with the current female-only vaccination (FOV) strategy. We used a dynamic transmission model, adapted to Hong Kong. The model estimates changes in HPV-related disease incidence and mortality, treatment costs (in 2019 Hong Kong dollars), quality-adjusted life years (QALY), and incremental cost-effectiveness ratios (ICERs) over a 100-year time horizon. The base case analysis compared FOV with the 9vHPV vaccine with routine GNV (coverage rate 70%) for the prevention of HPV-related diseases. Compared with a FOV approach, routine GNV with the 9vHPV vaccine is predicted to provide greater reductions in cumulative HPV-related disease incidence and mortality, as well as lower HPV-related treatment costs. In the base case analysis, the ICER was $248,354 per QALY for routine GNV. As compared with FOV, routine GNV fell below the cost-effectiveness ceiling of $382,046/year for Hong Kong. These results highlight the potential value of a routine GNV program with the 9vHPV vaccine among 12-year-olds in Hong Kong to reduce the public health and economic burden of HPV-related diseases.