The effects of a recreational soccer program (RSP) upon body composition, heart rate variability (HRV), biochemical markers, cardio-respiratory fitness, and endothelial function in obese adolescents were investigated. A randomised controlled clinical trial was conducted with 30 adolescents aged 12-17 years and body mass index (BMI) >2 standard deviations of WHO reference values, which were assigned to RSP (n = 10, 2 girls) and obese control (n = 10, 4 girls) groups. The 12-week RSP included 60-min sessions performed 3 times/week. BMI, waist circumference, blood pressure, blood glucose, lipid profile, insulin, C-reactive protein, HRV, and maximal oxygen consumption (VO2peak) were evaluated following standardised procedures. Body composition was determined by dual-energy X-ray absorptiometry and endothelial function by venous occlusion plethysmography. After intervention, RSP exhibited significant reductions in BMI (-0.7 ± 0.2 kg · m(-2)), waist circumference (-8.2 ± 1.4 cm), %body fat (-2.2 ± 0.4%), systolic blood pressure (-5.0 ± 2.3 mmHg), total cholesterol (-16.2 ± 5.8 mg · dL(-1)), triglycerides (-20.5 ± 12.9 mg · dL(-1)), C-reactive protein (-0.06 ± 0.01 mg · dL(-1)), insulin resistance (HOMA-IR, -1.4 ± 0.6), and sympathetic activity (LF, -13.9 ± 6.6 un) vs. controls (P < 0.05). Significant increase was observed in parasympathetic activity (HF, 13.9 ± 6.6 un), VO2peak (7.9 ± 2.8 ml · kg(-1) · min(-1)), and high-density lipoprotein cholesterol (11.0 ± 6.3 mg · dL(-1)) (P < 0.05). Vascular conductance (19.5 ± 8.1 ml · min(-1) · 100 ml, P = 0.005) increased and vascular resistance (-5.9 ± 2.4 ml · min(-1) · 100 ml, P = 0.041) decreased in RSP, but not in controls. A 12-week recreational soccer intervention was effective to improve biochemical, cardiovascular, and fitness health markers in obese adolescents.