Cervical cancer can be prevented by human papillomavirus (HPV) vaccination. However, parents can have concerns about vaccinating their daughters. Consequently, there is a need to identify prevalence and risk factors for HPV vaccine hesitancy among parents in Kenya. A descriptive cross-sectional study was conducted among parents with children aged 9–14 years attending a leading referral hospital in Kenya. Data on sociodemographic traits, HPV knowledge, beliefs and vaccine hesitancy were collected. Out of 195 participants, 183 (93.5%) were aged >30 years. Thirty-four (46.4%) of males and 39 (35.1%) of females did not know that the vaccine is given to prevent HPV infection. Encouragingly, levels of vaccine acceptance were high (90%) although one-third (37.9%) had a negative perception about the effectiveness of the vaccine, with vaccine hesitancy attributed to safety concerns (76%) and feelings that the child was too young (48%). Positive beliefs and knowledge of the vaccine were positively associated with parental willingness to vaccinate their children. Low levels of parenteral education and a younger age among mothers were negatively associated with willingness to vaccinate. Most parents (59%) would consult their daughters before vaccination, and 77% (n = 150) recommended early sex education. Despite low knowledge levels, there was high parental willingness to have their children vaccinated.