Adolescent obesity can impair cardiopulmonary function, vascular elasticity, endothelial function, and vago-sympathetic balance. While moderate-intensity continuous training (MICT) benefits cardiovascular health in obese adolescents, the effects of high-intensity interval training (HIIT) are less understood. We hypothesize that HIIT may be more effective than MICT in improving VO2peak, vascular elasticity, endothelial function, and vago-sympathetic balance in obese adolescent boys. Forty four participants were randomly assigned to the HIIT (10×1-min at 85%-95% peak HR, intersperse with 2-min active recovery at 60%-70% peak HR) or MICT (35min at 65%-75% peak HR) for an 8-week program. The primary outcome measured was the change in VO2peak with secondary outcomes including brachial-ankle pulse wave velocity (baPWV), flow-mediated dilation (FMD), and heart rate variability (HRV). Forty four adolescent boys with obesity (age, 14±1years old, body mass index, 31.6±1.3kg/m2) were enrolled and 43 (97.73%) completed the 8-week exercise. No significant difference of VO2peak was found between the HIIT and MICT group (p=0.243). There was no significant difference of baPWV between the groups (p=0.789). Change in FMD% was significantly higher in the HIIT group compared to the MICT group (p<0.001). The Change in HRV-high frequency (HRV-HF; p=0.009) and HRV-low frequency/high frequency (HRV-LF/HF; p=0.035) was significantly higher in the HIIT group compared to the MICT group. Among adolescent boys with obesity, 8-week HIIT and MICT had similar effects on improving VO2peak. HIIT may be superior to MICT to improve endothelial function and vago-sympathetic balance.