Intestinal parasitic infection are one the neglected tropical diseases listed by (WHO). They play a major role among all reasons to cause significant iron deficiency anemia and malnutrition especially among school going children located in rural areas. Our study mainly conducted to estimate the prevalence of intestinal parasitic infection and iron deficiency anemia among school going children. The main aim is to determine the prevalence of intestinal parasitic infection and also to correlate their comorbidities among school going children. A cross sectional study for one year was conducted at a tertiary care hospital which included school going children. In this study, 120 school going children was screened for intestinal parasitic infection and anemia. The stool examination was done by wet mount to detect the presence of ova/cyst and Hb% estimation by using XT 1000i. This 120 study participants with 56.6% boys and 43.3% girls were enrolled. The prevalence of intestinal parasitic infection is 7.5%. Entamoebahistolytica is the predominant protozoal parasite (33.3%) followed by hookworm (44.4%) and Hymenolepis nana (22.2%). Presence of anemia in present study population was 94.16%. To conclude, since intestinal parasitic infection can be controlled by following a few healthy hygienic practices like regular deworming, awareness on handwashing technique, intake of iron and folic acid supplement irrespective of the nutritional status, usage of proper toilets can reduce the incidence of iron deficiency anemia caused by intestinal parasitic infection in school going children.