This study investigated the effects of short-term and long-term periods (8 and 16 weeks) of high-intensity interval training (HIIT) on cardiovascular components, blood lipids, and 6-min walking test performance in obese young boys (age = 16.2 ± 0.7) with >34% body fat. The participants were split into two groups: severe obesity (SOG; n = 17) and moderate obesity (MOG; n = 16). All participants performed on a cycle ergometer for 16 weeks (3 times per week) of HIIT at 100% peak power output at the ventilatory threshold and recovered at 50% of peak power. Except for BMI, both groups improved all body composition measures after 16 weeks, with a higher percentage of change (Δ) in SOG. The 6-min walking test increased in both groups (p < 0.001). Furthermore, cardiovascular variables, blood lactate concentration at rest and after 5-min post-exercise, blood lipids, and insulin concentrations improved significantly in both groups. After 16 weeks, MOG significantly improved in HRpeak, blood glucose concentration, and rating of perceived exertion (RPE), but the percentage of change (Δ) was higher in SOG for all the other variables. SOG showed a higher (Δ) waist-to-hip ratio, maximum heart rate, resting heart rate, systolic blood pressure, blood lactate at 5-min post-exercise, and triglyceride concentrations after 8 and 16 weeks of training. In conclusion, a long-term HIIT program appears to be an appropriate training approach for obese boys with extra body fat. However, considering the RPE values, short-duration training sessions should be planned.