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Diarrhea, soil-transmitted helminth infection and malnutrition are leading causes of child mortality in low- and middle-income countries (LMICs). To reduce the prevalence of these diseases, effective interventions for adequate water, sanitation, and hygiene (WaSH) should be implemented. This paper describes the design of a cluster-randomized controlled trial that will compare the efficacy of four school-based WaSH interventions for improving children’s health literacy, handwashing, and nutrition. Interventions consisted of (1) WaSH policy reinforcement; (2) low-, medium-, or high-volume health education; (3) hygiene supplies; and (4) WaSH facilities (e.g., toilets, urinals, handwashing basins) improvements. We randomly allocated school clusters from the intervention arm to one of four groups to compare with schools from the control arm. Primary outcomes were: children’s health literacy, physical growth, nutrition status, and handwashing prevalence. Secondary outcomes were: children’s self-reported health status and history of extreme hunger, satisfaction with WaSH facilities, and school restrooms’ WaSH adequacy. We will measure differences in pre- and post-intervention outcomes and compare these differences between control and intervention arms. This research protocol can be a blueprint for future school-based WaSH intervention studies to be conducted in LMICs. Study protocols were approved by the ethics committees of the University of Bonn, Germany, and the University of the Philippines Manila. This trial was retroactively registered, ID number: DRKS00021623.