Abstract Background Intestinal parasites are the commonest cause of childhood diarrhea and malnutrition in Ethiopia. Information about intestinal parasites is the first fundamental step for designing intervention strategies against them. Hence, health planners can maximize their efforts. Information is scarce about intestinal parasites among children of under-five years of age in Boricha district. Therefore, this study aimed at assessing prevalence and factors associated with intestinal parasites among children of age 6 to 59 months in Boricha district, South Ethiopia. Methods A community based analytical cross sectional study was conducted among 624 children of age 6 to 59 months from January 1 to 30; in 2018. We have utilized two stage stratified sampling method. Firstly, simple random sampling was used to select sample Kebeles. Secondly, systematic random sampling method was used to select the study participants. Structured and interviewer administrated questionnaire was used to collect data. Parasitological examination of children’s stool was conducted microscopically. Data were entered into Epi-info, exported and analyzed by SPSS version 22. Logistic regression analysis was conducted to identify association between explanatory variables and outcome variable. Adjusted Odds Ratio (AOR) with 95% confidence interval (95%CI) was computed, and P-value