Little is known regarding racial/ethnic differences in human papillomavirus (HPV)-associated anogenital cancer among males. We examined age-adjusted incidence, late-stage diagnosis, survival and mortality of anogenital cancers among males in the United States. This population-based retrospective cohort study included 39,601 males diagnosed with HPV-associated invasive penile and anorectal cancers between 2005-2016 from the North American Association of Central Cancer Registries. We evaluated the association of race/ethnicity with outcomes using multivariable logistic regression, adjusted survival curves, and Cox proportional hazard modeling, adjusting for age, insurance, residential characteristics (metropolitan/non-metropolitan, area poverty, and geographic region), stage, and treatment. We also assessed interaction of race/ethnicity with other covariates in our late-stage and mortality models. Hispanic and Non-Hispanic (NH) Black males had highest age-adjusted incidence of penile and anorectal cancer, respectively. Higher odds of late-stage penile cancer was observed among NH Black (adjusted odds ratios [aOR] 1.22, 95% CI 1.07-1.39) and Hispanic males (aOR 1.17, 95% CI 1.04-1.31). Higher odds of late-stage anorectal cancer was observed among NH Black (aOR 1.25, 95% CI 1.14-1.36) and NH Other males (aOR 1.29, 95% CI 1.01-1.66). Compared to all other groups, NH Black males had the lowest cumulative and mean survival of both cancers and higher cancer-specific mortality (penile adjusted hazards ratios [aHR] 1.23, 95% CI 1.01-1.49; anorectal aHR 1.25, 95% CI 1.10-1.42). Racial/ethnic disparities in HPV-associated anogenital cancers differ depending on site. Interventions to increase HPV vaccination rates, early detection, and treatment of anogenital cancers in males are needed, particularly among men of color.