Many randomized controlled trials have investigated the role of school-based prevention interventions to reduce symptoms of anxiety and depression in young people. Systematic reviews have subsequently demonstrated a small, beneficial effect of these interventions when compared to a combined control group including usual care, no intervention, or waiting list controls. However, evidence from behavioral science and clinical psychology suggests control group choice may influence the relative effectiveness of non-pharmacological interventions. Here we explored whether separating this combined control group into distinct categories might influence the apparent effectiveness of preventive interventions. After updating an earlier review and network meta-analysis of preventive interventions for anxiety and depression in young people, we considered the impact of alternative control groups on estimates of effectiveness. This analysis was restricted to comparisons with cognitive-behavioral interventions only--the most common intervention used in the included studies. In targeted populations, for both anxiety and depression outcomes, the effect of a cognitive-behavioral intervention was larger when compared to waiting list controls than to usual curriculum, no intervention, or attention controls. For anxiety, the effect of no intervention was also considerably larger than waiting list control (standardized mean difference -0.37 [95% credible interval - 0.66, - 0.11], favoring no intervention). These results suggest that the beneficial effect of preventive school-based interventions previously observed in standard meta-analyses may be an artifact of combining control groups. Although exploratory, these findings indicate the impact of different control groups may vary considerably and should be taken into account when interpreting the effectiveness of interventions.