Background: Malnutrition, as a serious health problem in children, has an increasing prevalence in the developing countries. This study aimed to evaluate the anthropometric indices of primary school children in Iranshahr, a city in central region of Sistan and Baluchestan province, Iran. Methods: This cross-sectional study was conducted on a sample of 1000 6-14 year-old primary school children studying in 16 public and 5 private schools in Iranshahr city from May to June 2017. The sampling was done using multistage cluster random method. The school records were used to determine the students' ages. Their weight, height, and body mass index (BMI) were measured. Anthropometric indices including weight-for-age, height-for-age, and BMI-for-age were assessed using the National Center for Health Statistics/World Health Organization international growth reference and Center for Disease Control and Prevention (2000). Results: The rate of thinness was significantly higher in public than private schools (18.1% vs 1%; P < 0.0001). Overweight/obesity was lower in public schools’ children compared to students of the private schools (0.1% vs 9.3%; P = 0.007). The rates of stunting and underweight in public and private schools’ children were 50.2% vs. 53.3% (P = 0.11) and 46.6% vs 35% (P < 0.0001), respectively. Conclusion: Findings showed that although nutritional status was better in private schools than public schools, malnutrition is still a potential public health problem in this area. Therefore, the nutrition interventions are suggested at national and regional levels to increase the parents' awareness.