Perceived risk for HIV acquisition among gay, bisexual, and other men who have sex with men (GBMSM) may not align with their actual sexual HIV exposure. Factors associated with low/moderate perceived risk among GBMSM eligible for pre-exposure prophylaxis (PrEP) (based on their high estimated HIV exposure) have been poorly described in Latin America. This is a secondary analysis of a 2018 web-based cross-sectional survey in Brazil, Mexico, and Peru. Participants were ≥ 18 years old, cisgender men, not living with HIV, had sex with other men in the previous six months, and had an HIV Incidence Risk Index for MSM score ≥ 10. We performed a multivariable logistic regression to identify factors associated with low/moderate perceived risk for HIV acquisition for each country. A total of 9900 GBMSM were included, and the majority (85.7%) reported low/moderate perceived risk for HIV acquisition. The mean age was 28.8 (SD = 7.7) years, and 77.7% had high school or more. Having ≥ 5 sex partners, daily use of geosocial networking (GSN) apps, and having sex (including condomless insertive anal sex) with a person living with HIV decreased the odds of low/moderate perceived risk for HIV acquisition, but an HIV test in the last year increased the odds only in Mexico. Latin GBMSM with high sexual HIV exposure (eligible to use PrEP) showed a massive gap with their perceived risk. HIV prevention counseling should explore HIV testing history and the frequency of use of GSN apps to promote an objective self-assessment of HIV exposure among Latin GBMSM.