Intensifying storms and inter-annual El Niño events may increase psychological stress and worsen mental health. This study examines the relationship between flood exposure and long-term mental health symptoms among adolescents and young people in Peru, the world’s most affected country by El Niño. We analyzed community and self-reported survey data from the Young Lives Study to contrast mental health in 2016 among youth who lived in communities that experienced or did not experience flooding between 2013 and 2016. We pre-processed data on 1344 individuals in 93 communities, using optimal full matching on Mahalanobis distance with a propensity score caliper, and estimated relative risks to mental health scores in the general population of young people and among gender-stratified groups via quasi-Poisson regression. Exposure to floods did not yield conclusive differences in mental health scores in this sample. Further evidence is needed on mental health patterns over time, the influence of exposure severity, and the impact of disaster relief on symptomology in mounting an effective global health response.