The Philippines is among the most exposed countries to natural hazards. Little is known about impacts of different natural hazards on academic gains or losses of cohorts of school children. Data from 33,704 elementary and 6337 secondary public schools (2009–2014) on typhoons, flood, earthquakes, and use as an evacuation center were analyzed. Provinces that are heavily populated and located near inland bodies of water are vulnerable to floods and those in the eastern side of the country are most vulnerable to typhoons. Correlational analyses on hazard vulnerability and change in school performance reveal that repeated use of school structures as evacuation centers has negative impact on school performance. There is provincial variability in magnitude of association between hazard vulnerability and test score gains/losses. These results have important implications on disaster mitigation and management in relation to education.