Objective This study sought to evaluate the association between discrimination and having mental health problems in the past 12 months in the sexual minority population in Peru. Methods We conducted a cross-sectional analysis of a secondary database corresponding to the first LGBTI survey in Peru in 2017. We included adults who self-identified their sexual orientation as gay, lesbian, bisexual, pansexual, or asexual/others. Both the exposure and dependent variables were self-reported by the participants. Multivariable Poisson regression was used to determine the association by calculating adjusted prevalence ratios (APR) with 95% confidence intervals (95% CI). Results Out of 9760 respondents, more than two-thirds of the participants reported having been discriminated against or having experienced violence at some time in their lives (70.3%) and one-fourth reported having mental health problems (23.8%). In the multivariable regression model, the prevalence of mental health problems in the last 12 months was 72% higher for the group of individuals who experienced discrimination when compared with the group that did not experience discrimination (APR = 1.72, 95% CI 1.57–1.88). The association was stronger among who self-identified lesbians (APR = 2.08, 95% CI 1.65–2.64). Conclusion The prevalence of mental health problems and discrimination was high in this population. In addition, we found a statistically significant association between discrimination and the occurrence of mental health problems in the last 12 months.