We examined the effectiveness of a computerised decision-support tool (DST), designed for paediatric healthcare professionals, as a means to tackle childhood obesity. A randomised controlled trial was conducted with 65 families of 6–12-year old overweight or obese children. Paediatricians, paediatric endocrinologists and a dietitian in two children’s hospitals implemented the intervention. The intervention group (IG) received personalised meal plans and lifestyle optimisation recommendations via the DST, while families in the control group (CG) received general recommendations. After three months of intervention, the IG had a significant change in dietary fibre and sucrose intake by 4.1 and −4.6 g/day, respectively. In addition, the IG significantly reduced consumption of sweets (i.e., chocolates and cakes) and salty snacks (i.e., potato chips) by −0.1 and −0.3 portions/day, respectively. Furthermore, the CG had a significant increase of body weight and waist circumference by 1.4 kg and 2.1 cm, respectively, while Body Mass Index (BMI) decreased only in the IG by −0.4 kg/m2. However, the aforementioned findings did not differ significantly between study groups. In conclusion, these findings indicate the dynamics of the DST in supporting paediatric healthcare professionals to improve the effectiveness of care in modifying obesity-related behaviours. Further research is needed to confirm these findings.