BackgroundSchools provide a favorable setting for health education, however, the most effective school-based exercise mode for improving physical fitness remains unclear. This network meta-analysis was designed to assess and rank the comparative efficacy of six exercise modalities on physical fitness indicators in a school-based setting.MethodsAn online search of the Web of Science, PubMed, SPORTDiscus, and Scopus databases was conducted. Randomized and quasi-randomized controlled trials were considered. Outcomes included measures of anthropometry and body composition, muscular fitness, and cardiorespiratory fitness. Data were pooled with a random effects model using the frequentist framework.ResultsA total of 66 studies with 8,578 participants (48% girls) were included. High-intensity interval training was the most effective intervention reducing body mass index (mean difference (MD) = −0.60 kg·m−2, 95% confidence interval (95%CI) = −1.04 to −0.15,p= 0.009), elevating VO2max(MD = 3.59 mL·kg−1·min−1, 95% CI = 2.45 to 4.74,p< 0.001), and 20-meter sprint performance (MD = −0.35 s, 95% CI = −0.55 to −0.14,p= 0.001). Aerobic training had the highest probability of reducing waist circumference (standardized mean difference (SMD) = −0.60, 95% CI = −0.88 to −0.32,p< 0.001). Active video games emerged as a promising modality for improving countermovement jump (MD = 2.43 cm, 95% CI = 0.06 to 4.80,p= 0.041) and shuttle running performance (SMD = 0.86, 95% CI = 0.29 to 1.43,p= 0.003). Strength training was the best exercise mode for improving standing long jump performance (SMD = 1.03, 95% CI = 0.07 to 1.98,p= 0.035) while combined training was rated the first for decreasing body fat percent (MD = −2.56%, 95% CI = −4.73 to −0.40,p= 0.022) and increasing push-up repetitions (SMD = 3.59, 95% CI = 0.81 to 6.37,p= 0.012).ConclusionSchool-based exercise interventions have multiple effects on physical fitness. The findings of this study will help to inform physical education teachers and coaches how best to deliver exercise programs in a school setting. Since the study was limited by the original research, the conclusions will require further verification using high-quality randomized controlled trials.Systematic Review RegistrationPROSPERO, Identifier: CRD42023401963.