Aim: Most rheumatic diseases are caused by a complex interplay of genetic, physical, and environmental factors. Large-scale disasters affect all of these factors; however, their impact on rheumatic diseases are unknown. We aimed to investigate changes in anti-rheumatic drug prescriptions among victims and non-victims following the 2018 Japan flood. Methods: In this retrospective cohort study, we used data from the Japanese National Database of Health Insurance Claims, which included information on all drugs prescribed by physicians. We included all cases of prescription at medical institutions in disaster-stricken areas between July 2017 and June 2019. The newly initiated prescription of methotrexate (MTX, 2 mg tablets or capsules), which has been exclusively approved for rheumatoid arthritis, juvenile idiopathic arthritis, or psoriatic arthritis/ psoriasis in Japan, as well as those for other anti-rheumatic drugs within the first year after the disaster were evaluated for government-certified disaster victims and non-victims. Results: The number of individuals who had not been prescribed MTX before the disaster was 4,973,401, including 31, 006 victims. Among them, 14,908 (including 110 victims) had a history of MTX prescription after the disaster. In the MTX-naïve group, new MTX prescriptions within one year after the disaster were significantly more frequent in victims compared to non-victims (age- and sex-adjusted hazard ratio: 1.83; 95% confidence interval: 1.37–2.46). Similarly, a non-significant increase in prescriptions for conventional synthetic/biological disease-modifying anti-rheumatic drugs was observed. Conclusions: Victims of the 2018 Japan flood were more likely to be prescribed MTX for the first time.