Background: Human papillomavirus vaccination is a well-known global strategy for the prevention of cervical cancer. However, uptake of the vaccine varies between regions and countries of the world due to several discouraging factors. Although adolescents are at risk for cervical cancer, there are limited studies measuring vaccination practice of female adolescents in the study area. Objective: To assess human papillomavirus vaccination practice and its associated factors among secondary school female students in Nekemte town, Oromia region, Ethiopia, 2022 Methods and materials: A school-based cross-sectional study was conducted from May 13 to June 13, 2022 among female students in secondary schools in Nekemte town, Oromia region, Ethiopia. A total of 423 samples were selected using a computer generated simple random sampling technique. Data was collected using a structured and self-administered questionnaire. The study participants were informed of the need for this study. Epi Data version 4.6 was used for data entry and statistical packaging for social science (version 26) for data analysis. Binary logistic regression was calculated using the odds ratio with a 95% confidence interval. Variables with a p-value < 0.25 in the bi-variable analysis were taken into multi-variable analysis. Finally, variables with a p-value < 0.05 were declared as statistically significant. Result: The current study revealed that the magnitude of human papillomavirus vaccination practice was 52% (CI; 46.8-56.6) in the study area. Factors significantly associated with human papillomavirus vaccination practice were: having good knowledge of human papillomavirus and its vaccine (AOR = 5.79, CI; 3.34 - 10.03), having positive attitude towards human papillomavirus vaccination (AOR = 8.36, CI; 4.67 - 14.93), higher maternal education level (college and above) (AOR = 5.47, CI; 1.68 - 17.82) and urban residence (AOR = 4.12, CI; 1.86 - 9.31). Conclusion and Recommendation: in this study, the magnitude of human papillomavirus vaccination practice was low. Therefore, we recommend the Ethiopian Ministry of Health conduct mass HPV vaccinations and community sensitization to increase awareness and behavioral change education is necessary to enhance optimum coverage of the vaccine.