OBJECTIVE: To determine the impact of the 2018 Japan Floods, one of the largest water disasters in Japan, on the number of prescriptions for triptans and ergotamine (acute treatment). BACKGROUND: Natural disasters frequently occur worldwide and may cause psychological stress-related diseases. Acute migraine attacks can be triggered by psychological stress. Disaster victims are likely to experience tremendous psychological stress; however, the relationship between natural disasters and migraine attacks is not well investigated. METHODS: A retrospective longitudinal cohort study was conducted using the National Database of Health Insurance Claims in the hardest-hit areas of the disaster 1 year before and after the disaster. We included people between the ages of 15 and 64 years. Those who had a victim code that was certificated by a local government were assigned to the victim group, and others to the nonvictim group. For those who were not prescribed acute treatment before the disaster (i.e., group without previous acute treatment), the cumulative incidence of new prescriptions for acute treatment at 12 months of follow-up was calculated and compared between victims and nonvictims with survival analysis. RESULTS: Of 3,475,515 people aged 15 to 64 years enrolled in the study, 16,103 (0.46%) were assigned to the victim group. In the group without previous acute treatment, 111 (0.70%) of 15,933 victims and 14,626 (0.43%) of 3,431,423 nonvictims were newly prescribed acute treatment after the disaster, and new prescriptions for acute treatment were significantly more likely to occur in victims than in nonvictims (adjusted hazard ratio, 1.68; 95% CI, 1.39-2.02). CONCLUSIONS: The 2018 Japan Floods increased the number of prescriptions for acute migraine medications among victims, suggesting that acute migraine attacks occurred more frequently after a natural disaster.