Uniform school-based anemia programs may not adequately address differences in iron status, menstrual blood loss, diet, adherence barriers, and social support. This study evaluated a risk-stratified, multicomponent anemia prevention program among adolescent girls. In this parallel-group randomized controlled trial, 80 girls at SMP Negeri 6 Kendari City were classified as being at low, moderate, or high risk based on hemoglobin, ferritin, C-reactive protein, menstrual bleeding, dietary, adherence, nutritional, and social-support indicators, and were allocated 1:1 to the intervention or routine-services group. Intervention intensity increased according to risk level through education, reminders, counseling, supervised supplementation, support, and referral. Seventy-six participants completed the week-12 assessment, while all 80 were retained in the intention-to-treat analysis. Baseline anemia prevalence was 37.5% in each group. At week 12, adjusted hemoglobin was 0.40 g/dL higher in the intervention group (95% CI 0.12–0.68; Holm-adjusted p=0.010), and the adjusted ferritin geometric mean ratio was 1.28 (95% CI 1.08–1.52; Holm-adjusted p=0.010). Adherence of at least 80% was achieved by 82.5% of participants in the intervention group and 50.0% of controls (RR 1.65; 95% CI 1.17–2.32; p=0.004). Reductions in anemia (RR 0.50; p=0.118) and iron deficiency (RR 0.54; p=0.130) were not statistically significant. The program was associated with improved biomarkers and substantially higher adherence, but evidence of a reduction in anemia prevalence remained inconclusive. Multicenter trials with longer follow-up and economic evaluation are warranted.