Oral human papillomavirus (HPV) infections are a leading cause of oropharyngeal cancers. In 2015 and 2016, HPV vaccines became publicly funded for gay, bisexual, and other men who have sex with men (GBM) under 27 years of age in most Canadian provinces. Between 2017 and 2019, sexually-active GBM in Montreal, Toronto, and Vancouver were recruited through respondent-driven sampling. Participants aged 16 to 30 years were invited to self-collect oral rinse specimens for HPV testing. We estimated HPV prevalence in the oral tract overall and compared these by vaccination status. Among the 838 GBM with a valid oral specimen, 36.9% reported receiving ≥1 dose of HPV vaccine. Overall, oral HPV prevalence was 2.6% (95% confidence interval, CI: 1.5, 3.7%) for at least one HPV type and 1.2% (95% CI: 0.5, 1.9%) for any high-risk type. We detected quadrivalent (HPV 6/11/16/18) vaccine-preventable types in 0.3% (95% CI: 0.0, 1.0%) of vaccinated individuals and 1.1% (95% CI: 0.1, 2.0%) in unvaccinated individuals. Oral HPV prevalence was low in a population of young urban GBM in Canada of whom 37% were vaccinated. Findings serve as a benchmark for monitoring of vaccination impacts on oral HPV infection within this priority population.