Background and purpose Migraine and irritable bowel syndrome (IBS) share many similarities characterized by their epidemiology, periodic pain, lack of definable organic causes, trigger factors, comorbidities and proposed pathophysiology. In this retrospective case–control study, the association between migraine and IBS was investigated using a nationwide population‐based database in Taiwan. Methods The data were retrieved from the National Health Insurance Research Database (NHIRD) of Taiwan. In all, 14 117 newly diagnosed migraine cases were identified in a subset of the NHIRD and 56 468 migraine‐free individuals were randomly selected as the comparison cohort. The multivariate Cox proportional hazards regression model was used to explore the risk of IBS in migraine sufferers after adjusting for demographic characteristics and comorbidities. Results After adjusting for the covariates, the incidence of IBS was 1.95‐fold higher in the migraine cohort than in the comparison cohort (73.87 vs. 30.14 per 10 000 person‐years). The adjusted cumulative incidence of IBS was also higher in the migraine group than in the control group in the follow‐up years (log‐rank test, P < 0.0001). In addition, the risk was most prominent in the youngest group (<30 years old), exhibiting a 3.36‐fold increased risk (95% confidence interval 2.44–4.63) of IBS compared with the migraine‐free cohort. Moreover, the incidence of IBS in migraine sufferers tended to increase with the frequency of migraine diagnoses. Conclusion The current population‐based study demonstrated that migraine is associated with an increased risk of IBS after adjusting for comorbidities, particularly in the young population.