Purpose: The present study compared the appetite responses to an inpatient eccentric vs. concentric cycling training programs in adolescents with obesity. Methods: 24 adolescents with obesity (12-16yrs; Tanner 3-4) followed a 12-week multidisciplinary intervention (Phase1), after which they were randomized to concentric (CON) or eccentric (ECC) training for 12 weeks (Phase2). Assessment of anthropometrics, body composition (DXA), aerobic power (VO2max), energy (EI) and macronutrient intake, food reward, and subjective appetite were performed at baseline, and after Phase1 (T1) and Phase2 (T2). Results: Body mass, BMI, and fat mass (FM%) decreased in both groups (p < 0.001). FM% reduction was greater in ECC at T2 (-9.9%). EI did not change in either group at T1, but was greater at T2 relative to T1 in CON only (p < 0.001,+22%). There was no correlation between the change in body mass, FM%, fat-free mass and EI. Hunger (p = 0.002) and desire to eat (p = 0.001) were higher in CON vs. ECC with no time effects nor interactions. Prospective food consumption increased in both groups with no group effect nor interaction. Satiety was not different between groups or over time. In ECC, preference for high-fat foods increased (p = 0.03), and preference (p = 0.004) and implicit wanting (p = 0.016) for sweet foods decreased. Conclusion: Eccentric cycling as part of an inpatient multidisciplinary weight-loss intervention might help prevent increased ad libitum energy intake compared to concentric exercise training in adolescents with obesity, potentially through distinct effects of the food reward system.