The global prevalence of overweight and obesity among children has increased rapidly in the recent decades, including in Malaysia. Thus, development of effective interventions to prevent childhood obesity in Malaysia is urgently needed. This paper describes the study design of a 12-week multi-component, school-based nutrition education programme aimed at managing childhood obesity. The objective of Juara Sihat™ is to determine the effectiveness of a nutrition education programme in improving anthropometric status, knowledge, attitude and practice (KAP) of nutrition, eating habits and physical activity level among overweight and obese children. This quasi-experimental study involves two primary schools in Kuala Lumpur with similar demographic characteristics. Eligibility criteria of research participants are overweight and obese children aged 9 to 11 years. The main components of the Juara Sihat™ intervention are nutrition education classes on healthy eating and active lifestyle; physical activity sessions; and active involvements of parents and teachers. The control school does not receive any interventions. The primary outcome is BMI-for-age z-score, while other outcomes include waist circumference, body fat percentage, KAP of nutrition score, dietary intake, physical activity level, sedentary behaviour and biochemical profile. Outcome measures will be assessed at three intervals: baseline, post-intervention 1 (3-month follow-up), and post-intervention 2 (6-month follow-up). The Juara Sihat™ programme represents a promising approach to examining the effectiveness of a school-based childhood obesity intervention with strong empowerment of Parents’ and Teachers’ Association (PTA). We anticipate that this study may provide insights towards the development of more effective strategies in formulating childhood obesity interventions.