Migraine is considered to be a neurovascular disease that manifests as a throbbing headache, possibly caused by the activation of the trigeminovascular system. Several studies have supported the role of inflammation in the pathogenesis of migraine. Chronic periodontitis (CP) is an infectious inflammatory disease triggered by bacterial products evoking an immune response which could result in the destruction of the periodontium. However, little is known about the longitudinal association between CP and migraine. In this study, we designed a nationwide population-based cohort study to investigate the risk of migraine and CP exposure in Taiwan. In total, 68,282 patients with CP were identified from the National Health Insurance Research Database (NHIRD), and 68,282 comparisons were randomly captured and matched by age, sex, monthly income, urbanization and comorbidities. The association between CP exposure and migraine risk was evaluated by Cox proportional hazards regression models. In this study, 785 migraine patients were identified in the CP cohort, and 641 migraine cases were found in the non-CP cohort. The incidence rate of migraine was significantly higher in the CP cohort than the non-CP cohort (adjusted HR: 1.21, 95% CI: 1.09-1.34, < 0.001) during the 13-year follow-up period. Females had a 2.69-fold higher risk for migraine than males (95% CI: 2.38-3.04, < 0.001). In summary, CP is associated with an increased risk of subsequent migraine in Taiwan.