Introduction WHO recommends vaccination against HPV for girls before sexual debut. Uganda started HPV vaccination in 2008 as pilot programs in 2 districts, followed by national roll out in 2015. Despite the availability of vaccines against human papillomavirus (HPV) in Uganda in the period covered by the study, there was reported low HPV vaccine uptake and completion especially of the second dose in Uganda; with little information available on timely completion of HPV vaccine and the associated factors in Uganda. This study was therefore done to determine the HPV vaccine dose 2 completion and describe the possible factors associated with timely HPV vaccine completion and non-completion among girls of age 9–14 years attending the adolescent clinic at Mulago hospital. Methods A retrospective mixed methods study was conducted in Mulago National Referral hospital adolescent clinic. Data were mainly collected through review of charts and folders for clinic attendance by eligible girls and focus group discussions with eligible girls that completed the 2 doses of HPV vaccine on recommended/scheduled time. Results Out of the 201 girls studied, 87 girls (43.3%) had timely completion of the HPV vaccination. Knowledge about HPV infection and HPV vaccine benefits, positive peer influence and healthcare worker recommendation to get vaccinated at health facility level positively influenced timely completion of HPV vaccine. Among barriers to completion of HPV vaccine identified were: inadequate information about HPV infection and HPV vaccine, concerns about HPV vaccine efficacy and safety, unclear communication with adolescents/caregivers from healthcare workers and -stock out of the HPV vaccine. Conclusion Timely completion of the second dose of HPV vaccine among girls attending the adolescent clinic of Mulago hospital was low (at 43.3%) but higher when compared to earlier published reports. Interventions around improved social mobilization, enhanced outreach and static vaccination approach and education of eligible girls on HPV vaccination can help increase vaccine uptake.