Introduction: Adequate daily intake of fruits and vegetables is crucial for the prevention of chronic diseases. This study aimed to determine the effects of My Body is Fit and Fabulous at School (MyBFF@school) with nutrition education intervention (NEI) on the stages of change for fruit and vegetable intake among overweight and obese secondary school children based on the trans-theoretical model (TTM). Methods: This was a cluster randomised controlled trial involving 15 out of 415 eligible government secondary schools in central Peninsular Malaysia, which were randomly assigned into intervention (six schools; 579 school children) and control (nine schools; 462 school children). The intervention group was given NEI for 24 weeks, while the control group followed the existing school programme by the Ministry of Education. Results: There was no significant difference between the intervention and control groups for the stages of change, with majority at the maintenance stage after six months (intervention: 34.9%; control: 39.0%). The within group analysis showed a significant reduction after six months for those at the action stage (action and maintenance stage) from 68.0% to 60.4% in the intervention group and from 71.4% to 65.6% in the control group. However, there was a significant increase among those with adequate fruit and vegetable intake in the intervention group and no significant increase in the control group. Conclusion: MyBFF@school with NEI based on TTM provided acceptable changes in fruit and vegetable intake among overweight and obese secondary school children.