The government of Nepal initiated the Mid Day Meal Program (MDMP) to reduce hunger and increase educational outcomes, including health status. However, limited studies have been conducted on these issues covering the nutritional status of students at the lower basic level at community schools in Nepal. The main objective of the study is to determine the factors associated with malnutrition among children from community schools in Nepal. A school-based cross-sectional study was conducted in 98 (46 basic and 52 secondary) community schools from 44 municipalities in Nepal. Altogether, 2727 students participated in the questionnaire survey and anthropometric measurement. Data collection was performed on May 10-31, 2023. WHO Anthro plus and LMS (Lambda Mu and Sigma) parameters were used: weight for age for national health and nutrition survey recommended by CDC/National Center for Health Statistics for ages older than ten years to analyze nutritional status, including z scores. Descriptive analysis, including inferential analyses such as the chi-square test and logistic regression, was performed using IBM SPSS Statistics v25. The prevalence of weight-for-age Z-score[WAZ], height-for-age Z-score [HAZ], and body mass index-for-age Z-score [BAZ] were 72%, 75%, and 82%, respectively. Students with z-scores outside the range of ±2 were classified as malnourished. Of them, 27.3%, 23% and 16.6% were assessed as underweight, stunted and thin, respectively. Students' sociodemographic characteristics such as age, asex, family size and type, source of income, wealth status were significantly associated with malnutrition, while age group, gender, wealth status, residence setting, and geographical location were noted as significant predictors of nutritional status. The study found no statistical relationship between school feeding and good nutrition, questioning the quality of the midday meal program. The study concludes that existing school-based nutritional interventions need to be re-evaluated and re-designed since it is less potent to minimize malnutrition among students substantially. Policymakers could consider these findings when planning and implementing nutrition-related policies and programs.