Background: School children are at great risk of nutrition-related chronic diseases. Their eating pattern in school is influenced by the availability of food served within the school environment. The purpose of this paper was to determine the effectiveness of a canteen-based food nutrition intervention, designed according to the theory of planned behaviour, on the knowledge, perception and choices of healthy food among primary schoolchildren. Methods: This was a prospective intervention study using a two-group design. Six school canteens from the ninety-eight primary schools were randomly allocated to an intervention group or a control group. All the food handlers in the intervention group were given a twelve-week training course in food nutrition. On the completion of the course, 293 Standard Six students from these schools, were interviewed with a nutritional questionnaire on food in their school canteens. The training programme for the intervention group and the questionnaire for the students were developed and validated for the study, and a power calculation made for the sample size of students.Results: The students in both groups were homogeneous in gender and body mass. The mean body mass index (BMI) was 19.26 (SD: 0.38) and 19.47 (SD: 0.39) for the intervention and the control group respectively. There were more schoolchildren in the intervention group who purchased foods in school canteens (p 0.0036)of milk and milk products (p 0.034), and white rice (p<0.001). Fewer purchased fast food (p<0.001), and more had a better perception towards serving of healthy food (p 0.001). There were no significant differences in the knowledge level (p 0.095) and purchased fruit (p 0.557) between the groups. Conclusion: A school-based nutrition programme was associated with significant improvement in the perception of students towards foods served in school canteens and in their choices of healthy food. The study provided a framework for the design and implementation of future food nutrition intervention in school canteens.