Low cardiorespiratory fitness (CRF) is considered as an established risk factor for cardiovascular and metabolic disorders. However, the effectiveness of high-intensity interval training (HIIT) versus moderate-intensity continuous training (MICT) in children and adolescents remained uncertain. Electronic databases of the PubMed, EmBase, and the Cochrane library were searched for randomized controlled trials (RCTs) investigated the role of HIIT versus MICT for children and adolescents throughout December 2019. Sixteen RCTs involving a total of 543 children were selected for final meta-analysis. HIIT versus MICT showed high peak VO2 (weighted mean differences (WMD): 2.68; 95% confidence intervals (CIs): 1.81 to 3.55; P<0.001), and no evidence of heterogeneity and publication bias was detected. However, there were no significant differences detected between HIIT and MICT on the levels of peak heart rate (HRmax), fat mass, free fat mass, weight, body mass index, waist circumference, systolic blood pressure, diastolic blood pressure, glycemia, insulinemia, total cholesterol, high density lipoprotein, low density lipoprotein, triglycerides, HOMA-IR, HbA1c, and leptinemia. The findings of this study revealed that HIIT versus MICT showed a significant improvement in peak VO2 in children and adolescents. Further large-scale RCTs should be conducted to compare the long-term effects of HIIT versus MICT in children and adolescents.