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Introduction: The primary objective of the current study was to assess factors associated with Human Papillomavirus (HPV) vaccine initiation and compliance in a cohort of active duty US military service members (SM). Materials and Methods: We included active-duty participants aged 18-26 years from the Millennium Cohort Study, a longitudinal cohort study of over 200,000 military SMs. The eligible study population included 22,387 female SMs and 31,705 male SMs. Vaccination was assessed over the period 2006–2017. Logistic regression was used to estimate the odds of vaccine initiation and compliance (3 doses within a 1-year period) in relation to demographic, military, health, and behavioral characteristics. Results: Among female SMs, 37.8% initiated the vaccine and 40.2% of initiators completed the series within a year. Among male SMs, 3.9% initiated the vaccine and 22.1% of initiators completed the series within a year. Differences by sociodemographic factors, deployment status, branch of service, occupation, and smoking status–but not by selected mental health conditions–were observed. Conclusion: HPV vaccination uptake is subpar across all military service branches. Certain subgroups of SMs could be targeted to increase overall HPV vaccine coverage in the US military population. [ABSTRACT FROM AUTHOR]