Introduction: While eccentric (ECC) training appears to be more efficient than concentric (CON) training at improving body composition in adolescent with obesity, its impact on health-related quality of life (HRQOL) has never been studied. Objective: The aim of this study is to compare the effects of 2 cycling training modalities, i.e., ECC vs. CON, in adolescents with obesity on HRQOL and health perception (HP). Methods: A total of 24 adolescents with obesity, aged 12–16 years, were randomized to either a 12-week ECC or a CON cycling training program performed at the same oxygen consumption (VO2). Anthropometric measurements, body composition, maximal incremental tests, HRQOL (Vécu et Santé Percue de l’Adolescent [VSP-A], Medical Outcome Study Short Form [SF-36]), and HP were assessed at before and after training. Results and Conclusion: Both CON and ECC cycling trainings promoted significant improvements in BMI, VO2peak, total fat mass, and fat-free mass, with better improvements in body composition parameters in the ECC group (p < 0.05). The VSP-A total score increased after CON (p < 0.01) and ECC (p < 0.001) training, with better enhancement for the ECC group (p < 0.05). The SF-36 physical score increased after both CON (p < 0.01) and ECC (p < 0.001) trainings. The global HP score increased only after ECC training (p < 0.001). Except for the energy-vitality item, no significant correlation was found between changes in HRQOL and its subdomains and anthropometric, body composition, and functional parameters. Both ECC and CON cycling trainings are associated with positive changes in HRQOL and HP. However, ECC seems to induce greater improvements in HRQL and HP than CON cycling training, which is probably not due to the anthropometric, body composition, and functional changes.