Aim <p>The aim of this study was to evaluate the effects of the Informed Health Choices secondary school intervention on the ability of students in Rwanda to think critically and make informed health choices after 1 year.</p> Methods <p>This was a two-arm cluster-randomized trial conducted in 84 lower secondary schools from 10 districts representing five provinces of Rwanda. We used stratified randomization to allocate schools 1:1 to the intervention or control arm. One class in each intervention school had ten 40-min lessons taught by a trained teacher in addition to the usual curriculum. Control schools followed the usual curriculum. The primary outcome was a passing score (≥ 9 out of 18 questions answered correctly) for students on the Critical Thinking about Health Test completed 1 year after the intervention. We conducted an intention to treat analysis using generalized linear mixed models, accounting for the cluster design using random intercepts.</p> Results <p>After 1 year, 35 of 42 teachers (83.3%) and 1181 of 1556 students (75.9%) in the control arm completed the test. In the intervention arm, 35 of 42 teachers (83.3%) and 1238 of 1572 students (78.8%) completed the test. The proportion of students who had a passing score in the intervention arm was 625/1238 (50.5%) compared to 230/1181 (19.5%) in the control arm (adjusted odds ratio 7.6 [95% CI: 4.6–12.6], <i>p</i> &lt; 0.0001). The adjusted difference in the proportion of students with a passing score was 32.2% (95% CI 24.5–39.8%).</p> Conclusions <p>The IHC secondary school intervention was effective after 1 year. However, the size of the effect was smaller than immediately after the intervention (adjusted difference 32.2% vs 37.2%) due to decay in the proportion of students in intervention schools with a passing score (50.5% vs 58.2%).</p> Trial registration <p>Pan African Clinical Trial Registry (PCTR), trial identifier: PACTR202203880375077. Registered on February 15, 2022.</p>