Water, sanitation facilities and hygiene education in schools provides safe drinking water, improves sanitation facilities and promotes lifelong health. WASH in Schools significantly reduces hygiene-related disease, increases student attendance and learning achievement, and contributes to dignity and gender equality. The main objective of the study is to assess the effects of school sanitation, water and hygiene on the educational outcomes among children in urban and rural schools in Dire Dawa city administration in Ethiopia. A school based comparative cross-sectional study was employed; both qualitative and quantitative methods were used. Data were collected using structured questioners, key informant interview with teachers, observation checklist and focused group discussion tools were applied. In these study 4 schools, 834 students, 21 teachers and 12 Parent Teacher Association (PTA) were participated and secondary documents were reviewed. The data were analyzed using descriptive statistics and multivariate logistic regression method. In the finding, students in rural schools 0.6 times more likely to attain low educational outcome compared to the students in urban schools.