This study evaluated the effectiveness of the community-based organization (CBO)-private clinic service model in increasing human papillomavirus (HPV) vaccination uptake among unvaccinated men who have sex with men (MSM) in Hong Kong during a 12-month follow-up period. A CBO-private clinic model was implemented to promote HPV vaccination among Chinese MSM. A CBO with good access to MSM approached MSM aged 18–45 years who had never received an HPV vaccination, invited them to receive an online health promotion, and referred them to receive HPV vaccination at gay-friendly private clinics. A baseline survey and a follow-up evaluation at Month 12 were conducted. A total of 350 participants completed the baseline survey. Among 274 participants who were followed up at Month 12, 46 (16.8%) had taken up at least one dose of HPV vaccination. After adjusting for significant baseline characteristics, the perceived susceptibility (AOR:1.25, p = 0.002) and perceived severity (AOR:1.21, p = 0.003) of HPV and HPV-related diseases, perceived benefits (AOR:1.16, p = 0.03), self-efficacy to receive HPV vaccination (AOR:1.37, p = 0.001), and behavioral intention to take up HPV vaccination at baseline (AOR:6.99, p < 0.001) significantly predicted HPV vaccination uptake. The process evaluation of the program was positive. The CBO-private clinic service model was helpful in increasing HPV vaccination uptake among MSM.