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Objectives: The purpose of this study was to analyze the relationship between a school health promotion program and problem drinking behaviors. Methods: The participants in this study were 1st-5th grade students in secondary school in Lima and Callao, Peru. We conducted pre- and post-surveys in 2014 and 2017, respectively, to assess the effect of a school health promotion intervention. The school health promotion intervention was implemented from 2015 to 2017 in four schools, and two schools were taken as control groups in collaboration with the Korea International Cooperation Agency. Randomized stratified sampling was performed to analyze 971 participants in the experimental group and 585 in the control group. The homogeneity test was conducted before the intervention. A chi-square test and logistic regression analysis were performed. The participants in this study were 1 to 5 grade students in secondary school in Lima and Callao, Peru. We conducted a pre-intervention survey in 2014 and post-intervention survey in 2017 to assess the effect of a school health promotion intervention. The school health intervention was implemented from 2015 to 2017 in 4 schools, and two schools were taken as control groups in collaboration with Korea International Cooperation Agency (KOICA). A randomized stratified sampling was performed to analyze 971 subjects in the experimental group and 585 subjects in the control group. The homogeneity test was conducted before the intervention. Chi-square test and logistic regression analysis was performed. Results: First, 35.7% of the students had experienced drinking more than once in their lifetime and 59.2% had experienced drinking in the last year. Among the 556 students who had experienced drinking, 21.9% had CRAFFT scores of 2 or more for problem drinking. Second, there were differences in general and problem drinking based on “gender,” “academic performance,” “part-time job,” “depression,” “smoking,” “drugs,” “sexual experience,” “school truancy,” and “violence or harassment from school friends.” Third, the proportion of problem drinkers was 15.2% in the experimental group and 32.1% in the control group; problem drinking was significantly higher in the control group. Finally, the risk of problem drinking in the control group was significantly increased by about 2.8 times as compared with the group receiving the intervention through the school health promotion program. Conclusion: The school health promotion program had a statistically significant effect on the improvement of adolescent drinking behaviors. Schools should strengthen health promotion and education to stimulate comprehensive activities to prevent drinking, smoking, and other substance abuse among adolescents.