Background and aim: There are contradictory results from the effect of iron and zinc supplementation on cognitive functioning of children. We investigated the effects of supplementation of iron and zinc, alone or in combination, on academic performance of primary school children. Methods: The study was a randomized double-blind clinical trial in which 101 primary school children, (61 females and 40 males) were randomly supplemented for 4 months with iron (20 mg/d), zinc (20 mg/d), iron+ zinc (20 mg of each/d), or nothing. Mean of continuous grades of dictation, mathematics, and reading were used to determine the academic performance and teacher checklist of Jon-Quay was used for validity of the method. Data were analyzed by one-way ANOVA, independent t test, and paired t test. Results: Mean of grades before and after intervention in received iron group, zinc group, iron+ zinc group, and control group were 17.29±2.47 vs. 17.95±2.35 (P<0.05), 17.70±2.8 vs.18.10±2.02 (P<0.01), 17.78±1.79 vs. 18.38±1.77 (P<0.05), and 18.31±1.85 vs. 18.40±1.60 (P>0.05), respectively. One-whey ANOVA did not show any significant difference between academic performance grade changes of groups. Conclusions: Supplementation with iron alone, zinc alone and iron plus zinc improved academic performance.