The aim of this study was to examine the effects of school-based high-intensity interval training (HIIT) on cardiorespiratory fitness and visceral adipose tissue (VAT) in children with obesity. A total of 40 students (11.0 ± 0.6 years; 20 boys) were randomized into an intervention group (IG) and control group (CG). The IG group performed a 12-week HIIT intervention with three sessions per week. Each session included 18 min of training (three sets of eight bouts of 15 s run at 100% maximal aerobic speed (MAS) separated by eight bouts of 15 s recovery run at 50% MAS) in PE class; the CG group were instructed to continue their normal behaviours. All subjects had indices of body mass index (BMI), fat mass (FM), body fat percentage (%BF), fat free mass (FFM), VAT, and maximal oxygen uptake (VO2max) measured at baseline and post-intervention. The cooperation of students was high, and all 40 students were included in the final analysis. A significant group–time interaction was determined in body composition (p < 0.05), with a significant decrease in BM (−3.4 ± 1.4 kg, p = 0.001; η2 = 0.63), BMI (−1.7 ± 0.5, p = 0.001; η2 = 0.58), %BF (−3.3 ± 1.4, p = 0.001; η2 = 0.54), and FM (−3.2 ± 1.4 kg, p = 0.001; η2 = 0.69), and VAT (−22.4 ± 9.8 cm2; p = 0.001; η2 = 0.61) in the IG. Furthermore, VO2max exhibited a significant increase in the IG (4.5 ± 1.6 mL/kg/min, p = 0.001; η2 = 0.84) and CG groups (1.7 ± 1.1 mL/kg/min, p = 0.001; η2 = 0.44). Integrating regular school-based HIIT sessions is a suitable method to improve body composition, cardiorespiratory fitness, and physical activity in students with obesity.