Background: In low and middle income countries, malnutrition especially among children is an increasing health problem. Objectives: To assess the level of malnutrition and its associated factors among school children in a rural setting in Fayoum governorate, Egypt. Methodology: A school based cross sectional survey was conducted on rural school children (6-17years) 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 different nutritional indicators using WHO anthroPlus. Sociodemographic, lifestyles and dietary habits were collected using a pretested interview questionnaire. Results: Prevalence of Stunting (HAZ <-2SD), underweight (WAZ<-2 SD), and wasting (BAZ <-2SD) was 34.2%, 3.4% and 0.9% respectively, while obesity based on BMI z-score (BAZ >+2SD) was 14.9%. Prevalence of obesity was significantly higher in younger age group of 6-9 years old in comparison with older age groups. Prevalence of obesity was significantly higher in males versus females (16.7% versus 8.0% , p=0.021) in 10-13 years’ 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), while daily fruit consumption was a protective one with OR 0.614(0.439-859). 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) Conclusion: Malnutrition is highly prevalent in rural school children of Fayoum in line with the national prevalence and significantly associated with age, gender, , regularity of father’s employment in addition to dietary factors.