Background Intestinal parasitic infections (IPIs) have been major public health problems in low income countries primarily affecting school children. Previous studies in Ethiopia have shown high burden of intestinal parasitic infections in most children. In order to gain a deeper insight into the magnitude of the problem more information is needed from different localities where similar studies have not been conducted. The aim of this study was to assess the prevalence of IPIs and associated risk factors among school children in Jawi Primary School, Jawi town, north -west Ethiopia. Methods A cross-sectional study was conducted from April to June 2017 to assess the prevalence of IPIs and associated risk factors among Jawi Primary School children, Ethiopia. A total of 422 children were selected using age-stratified systematic random sampling technique. Stool samples were examined microscopically using direct wet-mount and formal-ether concentration techniques. A structured questionnaire was used to obtain information regarding the associated risk factors. Data were analyzed using SPSS version 20 and p value < 0.05 was taken as statistically significant. Results Of 406 students examined for IPIs, 235 (57.88%) were positive for one or more intestinal parasites. Single, double and triple infections were 41.9, 6.2 and 1.2%, respectively. Overall infection rate was slightly higher in males (51.85%) than in females (45.30%) though the difference was not significant. Higher prevalence rate (about 51–53%) was recorded among 6 to 18 years old children. Prevalence of Giardia lamblia was the highest (19.95%), followed by hookworm (13.8%), Schistosoma mansoni (10.3%), Entamoeba histolytica/dispar (5.9%), Hymenolepsis nana (4.2%), Taenia species (3%) and Ascaris lumbricoides (0.73%), in that order. Among the risk factors assessed, age, hand washing habit before meals, open field defecation habit, consistency of wearing shoes, habit of eating raw and unwashed vegetables, and finger nail cleanliness and trimming habit were found to be the most important predictors associated with high risk of IPIs ( p < 0.05). Conclusion High prevalence of IPIs among Jawi Primary school children demands improved health education on regular hand washing, latrine use, wearing shoes, cleaning finger nails, not crossing rivers with bare foot and avoiding eating raw vegetables. Electronic supplementary material The online version of this article (10.1186/s12879-019-3971-x) contains supplementary material, which is available to authorized users.