Malnutrition and improper nutrition may lead to physical and mental growth disorder and cognitive function. This study aims to determine the prevalence of malnutrition and its relationship with educational status among primary school children in Zahedan, Iran. Methods: During a cross-sectional study with a multi-stage random sampling method of 780 boy and girl students, first, second, and third grades of elementary school were included to study. Demographic and anthropometric of students were collected based on the sample size. Malnutrition was assessed according to World Health Organization indicators for the relevant age group. This assessment was based on body mass index (BMI) for age, height for age, and weight for age. Results: The prevalence of malnutrition was severe wasting, wasting, overweight, and obesity which were 0.8, 4.6, 6.4, and 5%, and severe underweight and underweight which were 0.9 and 4.7%, respectively. Severe stunting and stunting were observed in 0.3 and 2.8%, respectively. A statistically significant relationship was found between BMI for age, height for age and weight for age and educational status (P<0.05). Moreover, the educational status of students showed a statistically significant relationship with first and second-grade gender, birth rank, and Parent’s job and education (P<0.0001). Conclusion: Different forms of malnutrition among the students can negatively affect their performance, especially their educational status. Therefore, proper nutrition and increasing nutritional knowledge of primary school children and parents may help to prevent the problem