Introduction: Up to now, there is limited clarity on factors that determine the effectiveness of childhood obesity interventions. Objective: This study intends to uncover individual- and program-level predictors of BMI-SDS and fitness to achieve significant, sustainable health improvements. Methods: Data of 249 children with obesity or overweight who participated in an outpatient multidisciplinary program were analysed and compared to 54 waitlist controls. Linear regression models were used to examine associations between individual- and group-level variables and BMI-SDS and fitness. Results: Among intervention children, BMI-SDS decreased by 0.19 units and physical fitness increased by 11.5%, versus a BMI-SDS decrease of 0.07 and a 1.8% decrease in fitness in the control group. Participants who reported being physically active before the program start achieved greater improvements in BMI-SDS (β = -0.177, p < 0.05) and physical fitness (β = 0.174, p < 0.05) than inactive peers. BMI-SDS decreased significantly more for members of gender-heterogeneous groups (β = 0.194, p < 0.05) with a narrow age range (β = 0.152, p < 0.05). Conclusions: The program under review is effective in counteracting juvenile obesity. The results give reason to believe that forming mixed-gender groups with a small age range and providing increased support for reportedly inactive children may improve program effectiveness.