High-intensity interval training (HIIT) interventions are typically prescribed according to several laboratory-based parameters and fixed reference intensities to accurately calibrate exercise intensity. Repeated all-out printing efforts, or sprint interval training, is another form of HIIT that is prescribed without individual reference intensity as it is performed in maximal intensities. No previous study has performed a systematic review and meta-analysis to investigate the effect of HIIT and SIT on cardiometabolic health markers in children and adolescents. Moreover, previous studies have focused on single risk factors and exercise modalities, which may restrict their ability to capture a complete picture of the factors that could be affected by different interval interventions. The present study aimed to conduct a novel meta-analysis on the effects of HIIT and SIT on multiple cardiometabolic health markers in children and adolescents. An electronic search was conducted in three main online databases including PubMed, Web of Science, and Scopus were searched from inception to July 2024 to identify randomized and non-randomized control trials comparing HIIT and SIT versus the non-exercise control group in children and adolescents with mean age ranges from 6 to 18 years old on cardiometabolic health markers including fasting glucose and insulin, insulin resistance, triglyceride (TG), total cholesterol (TC), low-density lipoprotein cholesterol (LDL), high-density lipoprotein cholesterol (HDL), systolic blood (SBP) and diastolic blood (DBP) pressures. Standardized mean differences (SMD), weighted mean differences (WMD), and confidence were calculated using a random effect model. HIIT decreased insulin, insulin resistance, TG, TC, LDL, and SBP and increased HDL but did not decrease glucose and DBP. Furthermore, subgroup analyses show that insulin and insulin resistance were decreased by sprint interval training (SIT) and in those with obesity. Lipid profile mainly is improved by SIT and in those with obesity. Also, SBP was decreased by SIT and in those with obesity. Our results prove that HIIT is an effective intervention for improving cardiometabolic health in children and adolescents, mainly those with obesity. Specifically, SIT is an effective interval training mode in children and adolescents.