We encountered cases of headache exacerbation in migraine patients living in the Tokyo metropolitan area following the Great East Japan Earthquake in the present study. We investigated the effects of the disaster situation on patients with migraine headaches following the Great East Japan Earthquake as well as their physical symptoms and psychological states using a questionnaire. The questionnaire survey was also conducted to clarify the prevalence of patients with headaches prior to earthquakes. The recovery rate was 65.7% (71/108 people). The seventy-one patients with migraines included 68 female patients (95.8%) and 19 patients that had migraines with an aura (26.8%). The exacerbation of headaches was observed in 24.6% of the migraine patients after the earthquake. Furthermore, a degraded psychological state was noted in patients with worsening headaches who began taking medication for insomnia. However, the disaster situation did not directly affect headache symptoms. Some of the patients examined (7.0%) had headaches prior to earthquakes in the Tokyo metropolitan area. These results indicate that the exacerbation of headaches was observed in migraine patients who exhibited co-morbidities including insomnia and anxiety in the Tokyo metropolitan area away from the affected area. We also showed that some of these patients had headaches prior to earthquakes.