Fascioliasis is a zoonotic trematode infection that is endemic in the highlands of Peru. Chronic fascioliasis can be asymptomatic and remain undiagnosed for years. Chronic malnutrition in children, as manifested by stunting, leads to delayed cognitive development and lost productivity. We hypothesized that fascioliasis is among the factors associated with stunting in children from endemic areas. We conducted a cross-sectional study among children attending pre-school and school in 26 communities in the Anta province in the Cusco region of Peru. We conducted interviews to collect information on demographic, socioeconomic, and medical history. Blood was collected and tested for complete cell count and FAS2 ELISA for Fasciola antibodies. Three stool samples per participant were tested for parasites by Kato-Katz and Lumbreras rapid sedimentation methods. Chronic fascioliasis was determined by the presence of ova in stool. Children’s height, weight, and age were recorded and used to calculate height for age Z scores (HAZ). Three thousand children participated in the study. Nine percent (264) of children had at least one positive test for Fasciola infection, 6% (164) had chronic fascioliasis, and 3% (102) had only positive antibody tests. The median HAZ was-1.41 (IQR:-2.03 to-0.81) and was similar in males and females. Twenty six percent (776) of children had stunting with HAZ <-2. Children with chronic fascioliasis had a lower median HAZ than children without Fasciola (-1.54 vs.-1.4, p = 0.014). History of treatment for malnutrition, history of treatment for anemia, having other helminths in stool, lower socioeconomic score, living at a higher elevation, and fewer years of schooling of both parents were associated with a lower HAZ score. In a multiple regression analysis, older age and a lower socioeconomic score were associated with a lower HAZ score. While fascioliasis and other helminths were associated with lower HAZ, they were not independent of the socioeconomic score.