This study evaluated the effectiveness of ‘ENTREN-F’ –a multi-component, family system-based intervention-for managing paediatric obesity at National Health Primary Care. A 3-arm, parallel-design, single-blinded randomized controlled trial (RCT), 165 families were randomized: Arm 1) ENTREN-F(n = 62) is a 12-week cognitive-behavioural intervention (CBT) family system-based programme, addressing lifestyle changes, children's emotional and social development and the family system, Arm 2) ‘ENTREN’ (n = 52) is a CBT family-based programme for children and parents, not addressing the family system, and Arm 3) Control group (CG) (n = 51) covers individual behavioural monitoring. All children were clinical interviewed to assess a diagnosis. Their effectiveness was assessed against six-month changes in children's body mass index (BMI) z-score, children's psychological well-being, levels of expressed maternal emotion, depression symptoms, parental feeding practices, levels of physical activity and sedentary lifestyles. The maintenance of the changes was evaluated for two years. High-attendance rates for ENTREN-F (72.6% vs. 66% vs. 33%, respectively) indicated its greater acceptance. After programme completion, the BMI z-score reduced by .5 points in almost 50% ENTREN-F (n = 22/45), 21.9% ENTREN (n = 7/32) and 11.8% (n = 2/17) CG participants. There were no significant differences between the three trial arms for anthropometric, psychological, or family-related measures. At the two-year follow-up, both ENTREN-F and ENTREN showed similar long-term effectiveness without between-group differences, and weight trajectories were favourable. ENTREN-F appears effective for childhood obesity management; however, the COVID-19 pandemic limited the sample size. Also, the tendency towards multiple differences in child and family outcomes could not be statistically shown. It also provides further evidence of the role of psychological and family-related factors that may underlie the origin and maintenance of weight gain.