Diet composition is a key determinant of childhood obesity. While whole grains and micronutrients are known to decrease the risk of obesity, there are no interventions originating from Southeast Asia that emphasize whole grain as a strategy to improve overall quality of diet in combating childhood obesity. The GReat-Child Trial aimed to improve whole grain intake and quality of diet among overweight and obese children. It is a quasi-experimental intervention based on Social Cognitive Theory. It has a 12-week intervention and 6-month follow-up, consisting of three components that address environmental, personal, and behavioral factors. The intervention consists of: (1) six 30 min lessons on nutrition, using the Malaysian Food Pyramid to emphasize healthy eating, (2) daily deliveries of wholegrain foods to schools so that children can experience and accept wholegrain foods, and (3) diet counseling to parents to increase availability of wholegrain foods at home. Two primary schools with similar demographics in Kuala Lumpur were assigned as control (CG) and intervention (IG) groups. Inclusion criteria were: (1) children aged 9 to 11 years who were overweight/obese; (2) who did not consume whole grain foods; and (3) who had no serious co-morbidity problems. The entire trial was completed by 63 children (31 IG; 32 CG). Study outcomes were measured at baseline and at two time points post intervention (at the 3rd [T1] and 9th [T2] months). IG demonstrated significantly higher intakes of whole grain (mean difference = 9.94, 95%CI: 7.13, 12.75, p
< 0.001), fiber (mean difference = 3.07, 95% CI: 1.40, 4.73, p
= 0.001), calcium (mean difference = 130.27, 95%CI: 74.15, 186.39, p
< 0.001), thiamin (mean difference = 58.71, 95%CI: 26.15, 91.28, p
= 0.001), riboflavin (mean difference = 0.84, 95%CI: 0.37, 1.32, p
= 0.001), niacin (mean difference = 0.35, 95%CI: 1.91, 5.16, p
< 0.001), and vitamin C (mean difference = 58.71, 95%CI: 26.15, 91.28, p
= 0.001) compared to CG in T1, after adjusting for covariates. However, T1 results were not sustained in T2 when intervention had been discontinued. The findings indicate that intervention emphasizing whole grains improved overall short-term but not long-term dietary intake among schoolchildren. We hope the present trial will lead to adoption of policies to increase whole grain consumption among Malaysian schoolchildren.