Introduction: The aim of this study was to investigate the relationship between gender, birth weight, nutritional status, and iron status of children with their academic performance and cognitive function. Methods: Two hundred and fortynine children, seven to nine years of age, were recruited by systematic sampling from six primary schools in a rural area in Malaysia. Cognitive function was assessed by using Raven’s Coloured Progressive Matrices (R-CPM). Academic performance of the children was recorded from their school final examination results in four subjects including Malay language, English, Mathematics, and Science. Birth weight was recorded from the birth certificate, and nutritional status was determined by weight-for-age z score and height-for-age z score. Results: Girls had a significantly higher score in all the academic tests, but a lower cognitive score compared to boys. Nutritional status was found to be correlated significantly with academic performance. Academic and cognitive function scores were also found to be correlated significantly with birth weight, parents’ education, and family income. In a multivariate analysis, gender remained the significant predictor of academic function, and iron status and haemoglobin were the significant predictors of cognitive function, after controlling for other variables. Conclusion: The study showed that girls performed better academically than boys in rural Malaysia. Nutritional status, parents’ education and family income could be additional modifiable factors to improve academic performance of the children. More attention is needed to improve academic achievements of boys at their early school years.