This study evaluated the impact of packaged interventions for operation and maintenance (O&M) on the usability and cleanliness of toilets in public schools in the Philippines. In this cluster-randomized controlled trial, the divisions of Roxas City and Passi City were randomly assigned to the intervention or control group. Schools in Roxas City (n = 14) implemented the packaged O&M interventions; schools in Passi City (n = 16) formed the control group. Outcome variables were toilet usability—defined as accessible, functional and private—and toilet cleanliness, measured using the Sanitation Assessment Tool (SAT) and the Cleaner Toilets, Brighter Future (CTBF) instruments at baseline and at four months follow-up through direct observation of school toilets. SAT results showed that intervention schools had a 32.0% (4.6%; 59.3%) higher percentage of usable toilets than control schools at follow-up after full adjustment (p = 0.024). CTBF results found a similar result, although this was not statistically significant (p = 0.119). The percentage of toilets that were fully clean was 27.1% (3.7%; 50.6%) higher in intervention schools than in control schools after adjustment (p = 0.025). SAT results also showed an improvement in cleanliness of toilets in intervention schools compared to those in controls, but this did not remain significant after adjustment. The findings indicate that the additional implementation of O&M interventions can further stimulate progress towards reaching Water, Sanitation and Hygiene service levels aligned with the Sustainable Development Goals.