Background: Intestinal helminths infection mainly occurs in the tropics and sub-tropics and affects the health status of school children by causing anemia, malnutrition and also restrictions in physical and cognitive development. This study aimed to access the prevalence of intestinal helminths and associated risk factors among primary school children in Gedeo Zone, Southern Ethiopia. Methods: A cross-sectional study was conducted from February to April 2020. Stool samples were collected and processed by using Wet Mount (WM) and Formol-Ether Concentration (FEC) techniques. The Pearson’s chi-square and multivariate analysis was performed to verify the association between helminths and associated risk factors. Results: A total of 413 school children were participated. The mean age ± SD of the study participants was 10.7 ± 2.64 years. The overall prevalence of intestinal helminths was 27.3%. Ascaris lumbricoids was the most prevalent intestinal helminths 77 (18.6%) followed by Trichuris trichura 9 (2.2%) and Hook worm 15 (3.6%).Poor hand washing practice before meal (AOR=0.46; 95% CI: 0.232-0.915; P=0.027), drinking water from river (AOR=1.01; 95% CI 0.004-2.600; P=0.000), living in rural area(AOR=0.63; 95% CI: 0.397-0.915; P=0.052) and poor toilet use habit (AOR=0.45; 95% CI: 0.114-0.520; P=0.000) were factors significantly associated with intestinal parasite infections. Conclusions: The prevalence of intestinal helminths was high in the study area, 114 (27.3%). Therefore, intervention measures including periodic school-based deworming programmes needed to improve the health of school children.