Human Papilloma Virus (HPV) infection is a common, preventable, sexually transmitted disease with oncogenic potential and increasing incidence. This study aimed to gain an understanding of the knowledge and awareness of HPV, the HPV vaccine, and HPV-related cancers, and to evaluate the relationship between participant factors and HPV knowledge, vaccination uptake, and high-risk HPV (16/18) infection, among Indigenous Australians. Data from the 12-month follow-up of a longitudinal cohort study were utilized, involving 763 Indigenous Australian adults in South Australia. The data analysis found that the mean 7-item HPV knowledge tool (HPV-KT) score was 2.3 (95% CI: 2.1–2.4), HPV vaccination prevalence was 27.0% (95% CI: 23.6–30.5) and oral HPV 16/18 infection was 4.7% (95% CI: 3.2–6.2). Multivariable log-Poisson regression models showed ratios of approximately 1.5 times higher HPV-KT scores in females, previous recreational drug users, those who had self-rated as having excellent, very good or good general health and who had heard of HPV; and participants who were not HPV vaccinated had 0.8 times (MR = 0.8, 95% CI: 0.7–0.9) lower HPV-KT scores than their counterparts. The findings suggest that culturally safe education strategies are a necessary investment to improve vaccination coverage among Indigenous Australians and to reduce the impact of HPV and related cancers.