This study aims to identify an effective intervention group for the control of the intestinal helminth infection among school-age children in rural Nepal. We examined 1677 stool samples of school-age children from 25 schools and 1014 samples from 25 communities in rural Nepal. We used formalin-ether sedimentation technique for the microscopic examination of the stool samples and identified three major intestinal helminths: Ascariasis lumbricoides, hookworm and Trichuris trichiura. Our results revealed that the newly enrolled under-6-year-old children at the schools were more widely infected with at least one of the three major helminths than those in the communities (odds ratio [OR] 2.29). We detected a significant difference in the prevalence of A. lumbricoides (OR 1.70), hookworm (OR 2.57) and T.trichiura (OR 3.23) between under-6-year-old children at the schools and those at the communities. The study results suggest that an appropriate deworming programme is needed for the newly enrolled under-6-year-old children in the primary schools in Nepal.