Malnutrition is an increasing health problem among children in developing countries. We assessed the level of malnutrition and associated factors among school children in a rural setting in Fayoum Governorate, Egypt. A school based cross-sectional survey was conducted on children (6-17 years) in Manshit El Gamal village in Tamia district of Fayoum Governorate. Weight, height, and age data were used to calculate z-scores of the three nutritional indicators using WHO anthroPlus. Sociodemographics and lifestyles Data were collected. Prevalence of stunting, underweight, and wasting was 34.2%, 3.4%, and 0.9%, respectively, while obesity was 14.9%. Prevalence of obesity was significantly higher in younger age group of 6-9 years in comparison with older age and was higher in males versus females in 10-13-year-age group. Increasing age, reduced poultry consumption, and escaping breakfast were associated factors for stunting with OR (95% CI) 1.27 (1.17-1.37), 2.19 (1.4-3.4), and 2.3 (1.07-5.03). Younger age and regular employment of the father were factors associated with obesity (OR = 0.753; 0.688-0.824 and OR = 2.217; 1.4-3.5). Malnutrition is highly prevalent in Fayoum in line with the national prevalence and associated with age, gender, regularity of father's employment, and dietary factors.