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Background: In Ethiopia, the human papillomavirus vaccine has been introduced since 2018. Since the vaccination program targets girls age 9–13, the success of vaccination depends on the parental decision and their willingness to vaccinate their daughters. Therefore, a study on parental willingness to vaccinate their daughter and factors associated is needed. Objective: To assess parent's willingness to vaccinate their daughter against the human papillomavirus and its associated factors in Bench-Sheko Zone, southwest Ethiopia. Methods: A community-based cross-sectional study was conducted among 502 participants in Bench-Sheko Zone, southwest Ethiopia. The participants were selected using a systematic random sampling method. Frequency tables, mean and standard deviation were used to summarize the data. A binary logistic regression using bivariate and multivariable logistic regression analysis was used to identify factors associated with parental willingness to vaccinate their daughter. The level of significance was declared at P-value < 0.05. Results: Of the 502 participants interviewed, 399 (79.5%), 95% CI (76%, 83%) of parents were willing to vaccinate their daughter. The study found that primary education and above (AOR = 2.9, 95% CI [1.79, 4.95]), having good knowledge (AOR = 2.1, 95% CI [1.15, 4.10]) and positive attitude (AOR = 2, 95% CI [1.30, 3.41]) were significantly associated with parental willingness to vaccinate their daughter. Conclusion: This study found that there was a high parental willingness to vaccinate their daughter against the human papillomavirus in the study area. Primary education and above, having good knowledge and positive attitude were factors associated with parental willingness to vaccinate their daughter. Therefore, providing health information's regarding human papillomavirus vaccination with emphasis to raise community awareness should be designed especially less educated parents need to be targeted.