Introduction: The nutritional status of children determines their health, physical growth and development, academic performance and progress in life. However, nutritional status of the children in Nepal has become a major public health problem. Objectives: This study aims to “determine the factors affecting the nutritional status of children in Early Childhood Development Centers (ECDCs) of Pokhara City”. Method: A descriptive cross sectional approach was adapted for the study. Anthropometric parameters, namely weight and height, were measured among 282 children aged 2-5 years. Semi-structured questionnaires were used for mothers with face to face interview method. Data was analyzed by SPSS (version 20) and WHO Anthro-Software (version 3.2.2). Chi-square and Binary Logistic Regression Analysis were applied to measure associations. Results: Result indicated that among 282 children, 53.2% were males and 46.8% females with age range of 24 months to 59 months (mean age = 34.39 ±7.49 months). Among them, 32.6% were stunted, 16.0% were underweight and 18.1% were wasted. The prevalence of shunting and wasting was higher as compared to underweight in this Early Childhood Development Centre (ECDC). There was association between nutritional status and age (p= 0.001), sibling of the child (p=0.006), food taboo practice, (p=0.001), family economic status ( p=0.044), hand washing practice before feeding (p= 0.035), covering of food while cooking (p= 0.031) and vitamin A and De-worming given (p= 0.022). Conclusion: It is concluded that nutritional status is still a problem among children of two to five years of age in ECDC Pokhara Sub- Metropolitan City, Kaski. Major factors affecting nutritional status of children are increasing age, no colostrums feeding, food taboos, not covering the food during cooking, sibling of the child, vegetarian diet, and commercial food. These findings are of great importance because they demand potential actions that can be used to improve the nutritional status of children.