Abstract Background Intestinal parasitic infections are among the major public health problems in Sub-Saharan Africa. Their distribution is mainly associated with poor personal hygiene, environmental sanitation and limited access to clean water. Indeed, epidemiological information on the prevalence of various intestinal parasitic infections in different localities is a prerequisite to develop appropriate control measures. Therefore, the aim of this study was to assess the prevalence of intestinal parasitic infections and associated risk factors among schoolchildren. Method This school-based cross-sectional study was undertaken at the University of Gondar Community School from April 2012 to June 2012. Study subjects were selected using a systematic random sampling method. Data were gathered through direct interview by using a pretested questionnaire. The collected stool specimens were examined microscopically for the presence of eggs, cysts and trophozoites of intestinal parasites using direct saline smear and formol-ether concentration methods. Data entry and analysis were done using SPSS version 16 software. Result Out of 304 study subjects, 104 (34.2%) were infected with one or more intestinal parasites. The prevalence rate was 43 (32.1%) for male and 61 (35.9%) for female. The prevalence of intestinal parasites was high in age group of 10–12 years compared to other age groups. The predominant intestinal parasite was Hymenolepis nana, followed by Entamoeba histolytica/dispar and Ascaris lumbricoides with 42 (13.8%), 28 (9.2%), 18 (5.9%), respectively. Hand washing practice and ways of transportation were statistically associated with intestinal parasitic infections. Children in grades 1 to 3 had a higher prevalence of intestinal helminthic infection than those in grades 4 to 8 (p = 0.031). Conclusions Intestinal parasites were prevalent in varying magnitude among the schoolchildren. The prevalence of infections were higher for helminths compared to protozoa. Measures including education on personal hygiene, environmental sanitation, water supply and treatment should be taken into account to reduce the prevalence of intestinal parasites.