Protein–energy malnutrition is one of the leading causes of childhood morbidity and mortality in developing countries. The purpose of the present study was to measure the prevalence of stunting and its correlates among school children aged 6–12 years in the rural areas of southern Pakistan. We selected 1915 children aged 6–12 years enrolled in 32 primary schools in rural Sindh, Pakistan. Trained community health workers conducted child height and weight measurements and collected information from the parents. The Z-scores for the distribution of height-for-age, weight-for-age, and weight-for-height relative to those of National Center for Health Statistics/Center of Disease Control and prevention (NCHS/CDC) reference population were calculated. Out of 1915 children, 300 (16.5 per cent) were stunted. Female children compared to males were more likely to be stunted (prevalence ratio (PR) = 1.26; 95 per cent confidence interval (CI): 1.02–1.53). Children older than 7 years were more likely to be stunted (PR, 1.40; CI, 1.14–1.72). Fathers who were working as government employees (PR, 1.71; CI, 1.05–2.79), shopkeepers (PR, 2.00; CI, 1.22–3.26) and farmers (PR, 1.43; CI, 0.93–2.22) were more likely to have children who were stunted when compared to landlords. In rural areas of southern Pakistan, sex of child, age of the child, and father's occupation may be considered as important risk factors for stunting among school children aged 6–12 years.