We conducted a quasi-experiment to investigate whether a peer education intervention could result in positive sexual behavioral change outcomes in selected schools in Northern Malawi. The experimental participants (n = 158) were exposed to an HIV risk reduction intervention. The control participants (n = 147) were exposed to a Health Promotion Package. At 8 months, there were significant improvements in the intervention arm on several outcomes. The experimental group was 96% less likely to have sex than the control (OR = 0.04, CI = 0.01–0.20). Intervention participants were also 3.49 times likely to report condom use when they had sex (OR = 3.49, 95% CI = 0.96 to 12.65) and had lower odds of having multiple sexual partners. There were no significant differences on abstinence and the desire to have medical male circumcision (MMC). We suggest the intervention has potential efficacy to improve HIV risk reduction among adolescents in Malawi and perhaps in other similar settings.Trial registration: Pan African Clinical Trial Registry identifier: PACTR201612001889209.