Background Mental health problems among children and adolescents are an increasing public health concern, and physical activity has attracted attention as a scalable non-pharmacological intervention. However, the effects of physical activity may vary according to intervention content and participant characteristics, and clearer evidence is needed to guide the selection and implementation of interventions. Methods The protocol was registered in PROSPERO (CRD420251182579) and the review was conducted in accordance with PRISMA guidelines for systematic reviews and meta-analyses. The search was conducted in PubMed, Embase, PsycINFO, the Cochrane Library, Web of Science, and SPORTDiscus. Eligible studies included randomized controlled trials (RCTs) and quasi-experimental studies. Two reviewers independently performed study selection, data extraction, and risk-of-bias assessment. Standardized mean differences (SMDs) were pooled using a random-effects model, with prespecified subgroup, sensitivity, and publication-bias analyses. Results A total of 24 studies were included in the qualitative synthesis, of which 23 contributed 38 effect-size estimates to the meta-analysis. Physical activity interventions were associated with a small but statistically significant improvement in mental health outcomes (SMD = 0.19, 95% CI: 0.09–0.30; p = 0.0002), with moderate heterogeneity ( I 2 = 48%; Q = 71.14; p = 0.0006). Intervention type significantly moderated the effect (Chi 2 = 8.42; p = 0.04), with a relatively larger pooled estimate observed for mind–body interventions (SMD = 0.32, 95% CI: 0.15–0.49), followed by multicomponent/behavioral interventions (SMD = 0.18, 95% CI: 0.01–0.35), whereas the effects of sports/games and aerobic/fitness training were positive but not statistically significant. Baseline psychological risk status was also a significant moderator (Chi 2 = 4.87; p = 0.03), with larger effects in high-risk/trait groups (SMD = 0.31, 95% CI: 0.14–0.48) than in the general population (SMD = 0.16, 95% CI: 0.07–0.25). Sensitivity analyses supported the robustness of the findings. Conclusion Physical activity interventions were associated with small but significant improvements in mental health among children and adolescents. The findings suggest potentially larger benefits for mind–body interventions and for youth with elevated psychological risk, although these subgroup findings should be interpreted cautiously. These results support the targeted use of structured physical activity programs in school, public health, and early prevention settings. Systematic review registration https://www.crd.york.ac.uk/PROSPERO/view/CRD420251182579 , identifier: CRD420251182579.
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