Human papillomavirus (HPV) vaccination was introduced in the National Immunization Program (NIP) in Korea targeting girls aged 12 years to receive two doses of HPV vaccine to prevent cervical cancer. This study aimed to evaluate the factors that may influence parental decision to inoculate their daughters in Korea. A cross-sectional survey was conducted in 2020 by interviewing the parents of 2,000 nationally representative girls eligible for HPV NIP. By the daughters' status of HPV vaccination, the probabilities for each variable were compared with evaluate the factors that could affect parents' decision to inoculate their daughters with HPV vaccines. Compared with parents who were not vaccinated with HPV, parents who were vaccinated with HPV were 2.40 times more likely to decide to vaccinate their daughters with HPV. Parents who regularly undergo cervical cancer screening were 1.39 times more likely to decide to vaccinate their daughters with HPV than parents who do not receive regular checkups. Parents' perceived knowledge and perceived risk had a significant impact on their decision to vaccinate their daughters with HPV vaccines. Parents who had strong belief that HPV vaccine is safe in terms of adverse effects were 10 times more likely to decide to vaccinate their daughters against HPV. Parental factors including HPV-related health behavior and awareness were found to be associated with parental decision to vaccinate their daughters against HPV. To improve HPV vaccine uptake at 12 years, it is required to improve parental awareness on HPV through public communication supported by scientific-based evidence. Parental HPV vaccination and maternal regular cervical cancer screening were positively associated with parental decision to vaccinate their daughters against HPV. Parents' perceived knowledge of HPV vaccination and perceived risk of cervical cancer play an important role in determining whether their 12-year-old daughters will be vaccinated against HPV.