The human papillomavirus (HPV) vaccine reduces the prevalence of genital warts and the cancers they are associated with in males. However, the vaccination of males has always been neglected. Here, we performed a meta-analysis to comprehend the acceptability of the HPV vaccine in men and the factors impacting vaccination intentions. We searched PubMed, Web of Science, Embase, Ovid, CNKI, and Wan Fang up to 5 July 2023 for studies that reported HPV vaccine acceptance among men. A random effects model was used to obtain the pooled acceptance rate, and subgroup analysis was performed. Then, the influencing factors of HPV vaccination in males were analyzed. A total of 57 studies with 32,962 samples were included in the analysis. The overall acceptance rate of the HPV vaccine in general men was 47.04% (95% confidence interval [95%CI]: 39.23–54.93%), and 62.23% (95% CI: 52.93–71.10%) among those whose sexual orientation contained men. HPV vaccine acceptance rates differed significantly between the two populations (p = 0.01). The population with a medical background (46.23%, 95% CI: 40.28–52.24%) was more willing to be vaccinated. In comparison to the employed population (66.93%, 95% CI: 48.79–82.81%) and the unemployed (68.44%, 95% CI: 52.82–82.23%), vaccination acceptance rates were lower among students (47.35%, 95% CI: 37.00–57.81%) (p = 0.04). The most significant barriers to vaccination were perceived low risk of infection for themselves (45.91%, 95% CI: 31.73–60.43%), followed by vaccine cost (43.46%, 95% CI: 31.20–56.13%). Moreover, the recommendations from medical professionals (60.90%, 95%CI: 44.23–76.37%) and sexual partners (60.09%, 95%CI: 27.11–88.67%) were significant factors in promoting vaccination. Overall, acceptance of the HPV vaccine among general men was at a lower level, despite being slightly higher among men with a same-sex orientation. Popularizing knowledge about diseases and vaccines, encouraging medical professionals to recommend vaccines to men, or reducing the cost of vaccines may promote HPV vaccination.