Physical education classes often fail to include sufficient exercise intensity to induce changes in body tissue composition and physical fitness. Short-term high-intensity interval training protocols incorporated into physical education lessons are one possible solution to this problem. Existing studies have not examined how individuals differing in body mass index (e.g., normal-weight, underweight) respond to high-intensity interval training exercises. Therefore, this study aimed to evaluate the effects of a Tabata protocol on body composition measurements, aerobic capacity, and motor performance in underweight and overweight adolescents (the experimental groups) vs normal-weight adolescents (here regarded as the control group). The sample included 58 adolescents (28 boys, mean age = 16.2 years; 30 girls, mean age = 16.2 years) who completed the high-intensity interval training and the following set of measurements pre- and post- intervention: height, weight, body fat percentage and waist-to-hip ratio, physical efficiency index (based on the Harvard Step Test), agility (in 4 × 10 shuttle run test), and lower-limb muscle power in vertical jump. The results showed that high-intensity interval training was effective in reducing body weight, waist-to-hip ratio, and body fat percentage only in overweight individuals. Improvement in aerobic capacity was found only in underweight and overweight boys. Further research should focus on the development of customized exercise protocols and their adaptation to girls and assess the sustainability of the changes induced.