Background: Despite the introduction of the human papillomavirus (HPV) vaccine in China in 2016, the uptake rates of HPV vaccination were low. This study aimed to assess the status of HPV vaccination and identify associated factors influencing HPV vaccination among female medical college students in Hubei province. Methods: Using a multistage sampling method, this was a cross-sectional study conducted in six colleges in Hubei province in 2023. The data were collected by web-based online software. Multiple logistic regression was applied to explore factors associated with the uptake of the HPV vaccine. Results: Overall, 1148 female medical college students were enrolled in this study. Approximately 13.9% of participants reported receiving the HPV vaccine. About 85.5% of unvaccinated participants showed high levels of intention to receive an HPV vaccine in the future, and 89.1% of the participants had accessed information about the HPV vaccine from the Internet. Multiple logistic regression demonstrated that knowledge pertaining to HPV and the HPV vaccine, factors aligned with the protection motivation theory (PMT), and socio-variables such as the mother’s educational background and the presence of vaccinated family members were associated with the uptake of the HPV vaccine. Conclusion: Our findings revealed that the HPV vaccination was associated with the knowledge, perceived susceptibility, perceived response efficacy, and self-efficacy of HPV and the HPV vaccine among female college students. Therefore, increasing HPV and HPV vaccine knowledge within the framework of PMT may serve as an effective strategy to promote HPV vaccination rates among college students.