Background Anti-inflammatory cytokines, interleukin-4 (IL-4) and interleukin-13 (IL-13) modulate systemic energy metabolism through modifying body composition parameters. Hence, this study aimed at overweight adolescent boys to explore the effect of high intensity intermittent training (HIIT) on these anti-inflammatory cytokines and body composition parameters. Materials and methods Twenty overweight adolescent boys [aged: 18.0 ± 1.5 years, weight: 81.8 ± 4.3 kg, body mass index (BMI): 27.6 ± 0.8 kg/m2] completed this study. The subjects were randomly assigned into two groups of control (CG, n = 10) and training (TG, n = 10). Subjects in the TG performed their training sessions 3 days/week for 6 weeks. The baseline serum values of IL-4 and IL-13 and anthropometric features were measured 1 day before the beginning of exercise intervention and 1 day after the last training session in a fasting state. Results Six weeks of HIIT significantly increased the baseline serum levels of IL-4 (p = 0.022) and IL-13 (p = 0.014) in overweight adolescent boys. In addition, body weight (BW), BMI and body fat percent (BF%) were reduced in response to HIIT. Moreover, significantly negative correlations were found between changes of IL-4 and IL-13 with changes of BW, BMI and BF%. Conclusions HIIT seems to be an appropriate exercise modality for overweight adolescent boys to induce an anti-inflammatory cytokine response and, to improve body composition.