Human papillomavirus (HPV) poses a substantial but underestimated healthcare burden in Hong Kong. This study investigated factors affecting parental acceptance of HPV vaccination after the introduction of an immunisation programme for primary school girls. We assessed parental perceptions and related factors concerning HPV vaccination for both boys and girls. We conducted a cross-sectional survey between December 2021 and February 2022 among parents of Primary 4 to 6 students in Hong Kong. Our self-administered online survey collected data regarding socio-demographic characteristics, awareness and knowledge of HPV vaccination, attitudes towards HPV vaccination, and acceptance of HPV vaccination. Characteristics were compared between boys' parents and girls' parents. Factors associated with vaccine acceptance were analysed by multivariate logistic regression. We observed high awareness of HPV vaccination among boys' parents and girls' parents; however, they demonstrated relatively poor knowledge of HPV and the HPV vaccine. An alarming low HPV vaccination uptake rate was also observed. Attitudes towards the HPV vaccine were similar between parent groups. A majority of parents believed that the HPV vaccine was safe and effective in preventing infection. Parents of boys showed lower HPV vaccine acceptance. Factors associated with acceptance differed between parent groups. High awareness of HPV and HPV vaccine is predictive of vaccine acceptance. Boys' parents are less likely to accept HPV vaccination and emphasis should be placed on addressing potential HPV vaccine hesitancy in this group. Public education should also aim to raise awareness of government vaccination programme, and implementation of catch-up vaccination programme to school children beyond primary school should be considered.