Female genital mutilation is still a serious health problem in Ethiopia. Female genital mutilation conceptualizes harmful traditional practice and is among existing traditional attitudes and practices on practice in different corners of the world. Other than demographic and health survey data, studies showing the prevalence of female genital mutilation is scarce and in some areas nonexistent. Its existence is only, time and again recognized as the practice has various health, social and psychological adversities. This study team found it imperative as the problem warranty study with the aim to assess prevalence of female genital mutilation (FGM) as well as identifying its associated factors among high school students. Institution based cross sectional study design was employed. 95% confidence level and 3% margin of error were used to study the magnitude and associated factors of FGM among 798 high school and preparatory students. A multi stage sampling procedure was employed to select female students in the schools. This research showed percentages and association among the variables by univariate, bivariate and multivariate analysis. )], respectively were independently associated to higher prevalence of female genital mutilation. Irrespective of different forms of interventions in the country, the prevalence of female genital mutilation is still very high in the study area. This study thus revealed that palatable and very convenient intervention strategies need to be crafted to curb the problem at large and for those rural villagers who are at higher risk in particular.