PURPOSE: 1) To investigate the effectiveness of school-based high-intensity interval training (HIIT) interventions in promoting health outcomes of children and adolescents compared with either a control group or other exercise modality; and 2) to explore the intervention characteristics and process outcomes of published school-based HIIT interventions. METHODS: We searched Medline, Embase, CINAHL, SPORTDiscus, and Web of Science from inception until 31 March 2021. Studies were eligible if 1) participants aged 5-17 years old; 2) a HIIT intervention within a school setting ≥ 2 weeks duration; 3) a control or comparative exercise group; 4) health-related, cognitive, physical activity, nutrition, or program evaluation outcomes; and 5) original research published in English. We conducted meta-analyses between HIIT and control groups for all outcomes with ≥ 4 studies and meta-regressions for all outcomes with ≥ 10 studies. We narratively synthesised results between HIIT and comparative exercise groups. RESULTS: Fifty-four papers met eligibility criteria, encompassing 42 unique studies (35 randomised controlled trials; 36 with a high risk of bias). Meta-analyses indicated significant improvements in waist circumference (mean difference (MD) = -2.5cm), body fat percentage (MD = -1.7%), body mass index (standardised mean difference (SMD) = -1.0), cardiorespiratory fitness (SMD = +1.0), resting heart rate (MD = -5bpm), homeostatic model assessment-insulin resistance (MD = -0.7), and low-density lipoprotein cholesterol (SMD = -0.9) for HIIT compared to the control group. Our narrative synthesis indicated mixed findings between HIIT and other comparative exercise groups. CONCLUSION: School-based HIIT is effective for improving several health outcomes. Future research should address the paucity of information on physical activity and nutrition outcomes and focus on the integration and long-term effectiveness of HIIT interventions within school settings. TRIAL REGISTRATION NUMBER: PROSPERO CRD42018117567.