Gastrointestinal diseases are major contributors to mortality among children globally, causing one in 10 child deaths. Although most deaths are in children aged ≤ 5 years, the burden of disease in school-aged children is still considerable and contributes to high rates of school absenteeism. This study investigates behavioral and structural risk factors associated with diarrhea and/or vomiting among schoolchildren in Myanmar. Cross-sectional data from a school-based multistage cluster sample of grade 4 and 5 students were analyzed to explore water, sanitation, and hygiene (WASH) facilities and hygiene-related practices of students in monastic schools in Myanmar. The outcome of interest was student self-reported diarrhea and/or vomiting in the past week. Random effects multinomial logistic regression models were used to explore correlates at the student and school level. A total of 2,082 students from 116 schools across eight states/regions were included. Of these, 11% (223) self-reported at least one episode of diarrhea only, 12% (253) at least one episode of vomiting only, and 12% (244) diarrhea and vomiting in the past week. Independent risk factors associated with the outcome included poor availability of handwash stations, no access to a septic tank toilet, inconsistent toilet use, and lower student grade. These findings highlight the importance of having an adequate number of handwash stations for students, the provision of septic tank toilets, and consistent toilet use. Future WASH programs need to target not only the provision of these WASH facilities but also their utilization, particularly among younger school-aged children.