Background: Human papillomavirus (HPV) is the putative case of cervical cancer. However, uptake of HPV vaccination is reportedly low in Uganda. This study explored the predictors of HPV vaccination uptake among female adolescents aged 15-18 years in Gulu Municipality, in northern Uganda. Methods: This was an analytical cross-sectional survey that was conducted among adolescents aged 15-18 years in Gulu Municipality. A structured questionnaire was used. Data were analyzed using Statistical Package for the Social Sciences (SPSS) version 25. Descriptive statistics and a log binomial model were used to analyze the factors associated with HPV vaccination uptake. Results: Less than a quarter of the female adolescents (22%) aged 15-18 years in Gulu municipality, Gulu district, had been vaccinated with the human papillomavirus vaccine. HPV vaccination uptake was lower by 23% among adolescents who stayed with their mothers only (aPR = 0.769, CI = 0.595-0.995, P = 0.046), and by 14% among adolescents whose parents were unmarried (aPR 0.859, CI = 0.776-0.951, P=0.003). Conclusion:This study reports a low HPV vaccination coverage among adolescents in Gulu Municipality, which is associated with parental perceptions and marital status. Efforts to increase uptake should focus on parents of adolescents.