Introduction: Female genital mutilation is the removal of a woman's external genitalia in whole or in part for a non-obvious medical reason. Female genital mutilation causes short- and long-term complications like bleeding, pain, infection and exposes girls to sexually transmitted diseases. The determinants of female genital mutilation among children under the age of five have received less attention. As a result, the purpose of this study was to determine the factors that influence female genital mutilation in children under the age of five. Methods: A community-based unmatched case control study design was used. The study participants were chosen using computer-generated simple random sampling technique. With a ratio of 1:4 between cases and controls, 323 participants were recruited. Data were collected using an interviewer-administered questionnaire. The association between each independent variable and the dependent variable was determined using binary logistic regression. In a multivariable analysis, variables were considered statistically significant if they had a P-value of less than 0.05 at a 95% confidence interval. Results: In this study, mothers' circumcision status (AOR = 4.6; 95% CI: 2.29-9.25), mothers who had an unfavorable attitude (AOR = 4.15; 95% CI: 1.96-8.82), households in the poorest wealth quintile (AOR = 3.65; 95% CI: 1.2-11.54), mothers who had inadequate knowledge (AOR = 3.31; 95% CI: 1.51-7.25) and antenatal care visit of mothers (AOR = 2.46; 95% CI: 1.03-5.83) were found to be determinant factors of female genital mutilation. Conclusion and Recommendation: Mothers' circumcision status, mother's attitude, wealth quintile, knowledge of mothers, and number of antenatal care visits were factors associated with female genital mutilation. Regular awareness-building on the impacts of the practice and special attention to the mother's attitude are important to eliminate female genital mutilation.