The aim of this study was to assess the effects of a high intensity interval training (HIIT) program on anthropomorphic and cardiometabolic variables in schoolchildren with overweight and obesity. A total of 443 schoolchildren (age: 6.37 ± 0.65 years) took part in this study. The experimental group (EG; n = 295; age = 6.40 ± 0.64 years) was compound with children with overweight and obesity, whereas children with normoweight were included in the control group (CG; n = 148; 6.31 ± 0.67 years). The EG performed a training program based on HIIT two times per week for 28 weeks (56 sessions), whilst the CG performed their habitual physical education classes based on the national curriculum. Body mass index (BMI), waist circumference, body fat, ∑ 4 skinfold fat, waist to height ratio, waist circumference, and cardiometabolic risk were measured. The dependent variables were analysed by two-way analysis of covariance (ANCOVA 2 × 2). To analyse the percentage differences between groups, the chi-square test was used. P-value was set at p < 0.05. Significant differences were found in the EG in BMI, waist circumference, body fat, ∑ 4 skinfold fat, and waist to height ratio. In conclusion, an HIIT training program can be an effective tool for improving anthropomorphic variables and reducing cardiometabolic risk in schoolchildren with overweight and obesity.