Introduction: This paper discussed the effectiveness of “Healthy Kids Programme (HKP)”, specifically in improving the body weight status as well as knowledge, attitude and practice (KAP) of the children. Methods: In this longitudinal intervention study, a total of 12 primary schools in Klang Valley were randomly selected and divided into intervention and control groups. There were 386 standard three children participated at baseline. All children in the intervention group participated in the HKP that was conducted by nutritionists. The evaluations included the pre- and post-Immediate Impact survey (IIS) (every topic), and changes in nutrition KAP survey and anthropometric assessment of the children at the beginning and end of every year for three years. Results: School children in intervention group reported with an increased in the IIS score for each topic and achieved a significantly higher mean nutrition knowledge score than those in the control group over time. There were no significant differences in mean attitude and practice scores between two groups after the intervention. Children in the intervention group had lower rates of overweight and obesity (pre-test: 27.3%; post-test: 32.5%) than their counterpart (pre-test: 26.6%; post-test: 44.0%). Conclusions: The HKP is effective in improving nutrition knowledge of the children. A lower rate of overweight and obesity was observed in intervention group than control group. This approach will contribute towards inculcating healthy eating and active lifestyle habits among Malaysian children that bring about long-term health benefits.