BACKGROUND: Little is known about penile high-risk human papillomavirus (hrHPV) among men who have sex with men (MSM) in low- and middle-income countries. We aimed to determine the incidence, clearance, and persistence of penile hrHPV among Rwandan MSM. METHODS: We enrolled 350 MSM (345 with valid human papillomavirus [HPV] results) aged ≥18 years. At each visit (6-12 months apart), we collected penile PreservCyt specimens and blood for HPV and HIV testing, as well as sociodemographic and behavioral variables. HPV testing was performed with the Ampfire assay. Penile hrHPV incidence and clearance per 1000 person-months of follow-up, as well as prevalent and incident persistence, were computed and compared by HIV status. RESULTS: The mean (SD) age was 27.7 (6.7) years and 19.4% were living with HIV. Penile hrHPV incidence was 34.8 (95% CI, 29.1-41.8) per 1000 person-months of follow-up. HPV-16 (11.7; 95% CI, 9.26-14.9) and HPV-59 (6.1; 95% CI, 4.52-8.39) had the highest incidence rates. Prevalent and incident persistence was 47.5% and 46.6%, respectively. HPV-66 (33.3%), HPV-52 (30.8%), and HPV-16 (29.2%) had the highest prevalent persistence and HPV-33 (53.8%), HPV-31 (46.7%), and HPV-16 (42.6%) the highest incident persistence. No differences were found by HIV status except for HPV-45 (higher in MSM with HIV). CONCLUSIONS: We found high incidence and prevalent/incident persistence of penile hrHPV among Rwandan MSM. This highlights the importance of preventive strategies for HPV-associated anogenital cancers.