Men living with HIV are at significantly higher risk of persistent high-risk human papillomavirus (hrHPV) infections and related diseases, including anal cancer. The optimal approach for anal cancer prevention remains unclear. In addition, limited knowledge and training among healthcare providers further hinder the implementation of effective screening and management strategies. To describe hrHPV prevalence and cytological abnormalities in men living with HIV and identify educational gaps in provider knowledge, this cross-sectional study recruited 178 men living with HIV (aged 18–60 years) from an HIV care clinic in Morelos, Mexico. Participants provided anal canal samples for hrHPV DNA testing and cytological evaluation. Descriptive statistics were used to report prevalence rates for hrHPV genotypes and cytological abnormalities. hrHPV prevalence was 80.9%. LSIL was most common (39.87%), with HSIL detected in 3.27%. The high prevalence of hrHPV and associated cytological abnormalities in men living with HIV underscores the need for educational programs to enhance provider knowledge and skills in HPV vaccination, screening, and management. Targeted training for physicians and other HIV care providers can address gaps in prevention and care, ultimately reducing the burden of HPV-related diseases in this high-risk population. The study may have implications for similar special populations with high HIV and HPV infection rates.