The benefits of eccentric (ECC) training on fat mass (FM) remain underexplored. We hypothesized that in obese adolescents, ECC cycling training is more efficient for decreasing whole-body FM percentage compared to concentric (CON) performed at the same oxygen consumption (VO2). Twenty-four adolescents aged 13.4 +/- 1.3 years (BMI > 90th percentile) were randomized to ECC or CON. They performed three cyclo-ergometer sessions per week (30 min per session) for 12 weeks: two habituation, 5 at 50% VO2peak, and 5 at 70% VO2peak. Anthropometric measurements, body composition, maximal incremental CON tests, strength tests, and blood samples were assessed pre- and post-training. Whole-body FM percentage decreased significantly after compared to pretraining in both groups, though to a larger extent in the ECC group (ECC: -10% vs CON: -4.2%, P < 0.05). Whole-body lean mass (LM) percentage increased significantly in both groups after compared to pretraining, with a greater increase in the ECC group (ECC: 3.8% vs CON: 1.5%, P <0.05). The improvements in leg FM and LM percentages were greater in the ECC group (-6.5% and 3.0%, P = 0.01 and P < 0.01). Quadriceps isometric and isokinetic ECC strength increased significantly more in the ECC group (28.3% and 21.3%, P < 0.05). Both groups showed similar significant VO2peak improvement (ECC: 15.4% vs CON: 10.3%). The decrease in homeostasis model assessment of insulin resistance index was significant in the ECC group (-19.9%). In conclusion, although both ECC and CON cycling trainings are efficient to decrease FM, ECC induces greater FM reduction, strength gains, and insulin resistance improvements and represents an optimal modality to recommend for obese adolescents.