A school-based water, sanitation, and hygiene (WASH) intervention in the Philippines was evaluated. Students and households from four schools that received the WASH intervention (intervention schools) were compared with four schools that had not (comparison schools). Knowledge of critical handwashing times was high across all schools, but higher in intervention schools. Students reported higher rates of handwashing after toilet use (92% vs. 87%; RR = 1.06; p = 0.003) and handwashing with soap (83% vs. 60%; RR = 1.4; p < 0.001) in intervention versus comparison schools. In intervention schools, 89% of students were directly observed to handwash after toilet use versus 31% in comparison schools (RR = 2.84; p < 0.0001). Observed differences in handwashing with soap after toilet use were particularly marked (65% vs. 10%; RR = 6.5; p < 0.0001). Reported use of school toilets to defecate (as opposed to use of toilet elsewhere or open defecation) was higher among intervention versus comparison schools (90% vs. 63%; RR = 1.4; p < 0.001). Multilevel modelling indicated that students from intervention schools reported a 10-fold reduction in odds (p < 0.001) of school absence due to diarrhoea. In addition to school-based findings, self-reported handwashing at critical times was found to be higher among household members of students from intervention schools. This school-based WASH program appeared to increase knowledge and hygiene behaviours of school students, reduce absences due to diarrhoea, and increase handwashing at critical times among household members.