Summary What is already known about this subject Aerobic exercise training is frequently used to reduce risk factors for cardiovascular disease in obese adolescents. However, there is no consensus on how the intensity of exercise affects blood pressure and heart rate variability (HRV). What this study adds The current study shows that high-intensity exercise training is able to decrease heart rate and enhance HRV likely playing a role in improving cardiac autonomic modulation. However, it does not influence the reduction in blood pressure. Background Aerobic exercise improves cardiovascular health in general, but whether the impact varies with exercise intensity is not clear. Objective The aim of the current study was to compare the effects of a high-intensity aerobic exercise training (HIT) vs. a low-intensity aerobic exercise training (LIT) on blood pressure (BP), heart rate (HR) and heart rate variability (HRV) in obese adolescents. Methods Forty-three (13-18 years) Tanner stage (III-IV) matched obese adolescents were studied in a randomized trial of either HIT (corresponding to the ventilatory threshold I; n = 20) or LIT (corresponding to 20% below the ventilatory threshold I; n = 23) programme for a period of 6 months. All participants also received a multidisciplinary therapy that included nutritional, psychological and clinical counselling. Both HIT and LIT sessions were isocaloric, with energy expenditure set at 350 kcal. BP, HR and HRV were measured along with markers of body adiposity and insulin resistance before and after the respective interventions. Results The participants in both groups had similar physical and clinical characteristics. After the 6-month intervention, systolic, diastolic and mean BP decreased (P < 0.05, for all) similarly in both groups, whereas waist circumference, HR and HRV showed beneficial changes only in the HIT group (P < 0.05). Conclusion Aerobic exercise training set at a high intensity compared with the low intensity appears to have additional benefits on abdominal obesity and cardiovascular health in that it enhances the parasympathetic and autonomic modulation of the heart in obese adolescents.