Migraine is a common neurological disease that causes a variety of symptoms, most notably throbbing, which is described as a pulsing headache on one side of the head. Burning mouth syndrome (BMS) is defined as an intra-oral burning sensation. Currently, no medical or dental cause has been identified for BMS. Interestingly, neuropathic pain is a characteristic feature of BMS; however, it remains unclear whether migraine can cause BMS. We aimed to identify the association of migraine with the risk of developing BMS. We used a representative nationwide cohort sample of approximately 1 million patients from 2002 to 2013 to investigate the prospective association between migraine and BMS. A total of 4157 migraine patients (migraine group) and 16,628 patients without migraine (comparison group) were enrolled after 1:4 propensity score matching. The overall incidence of BMS was significantly higher in the migraine group (0.15 per 1000 person-years) than in the comparison group (0.05 per 1000 person-years). The adjusted HR for patients with migraine who reported BMS events during the 10-year follow-up period was 2.96 (95% confidence interval, 1.02-8.56), after adjusting for other covariates. However, in the subgroup analysis, the adjusted HR for BMS events did not show a significant difference between the migraine and comparison group according to sex, age, and comorbidities. This study suggests that migraine is associated with an increased incidence of BMS. Therefore, clinicians should be attentive to detect BMS at an early stage when treating patients with migraine.