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Background: Patients with inflammatory bowel disease (IBD) suffer from a wide range of comorbidities such as migraine. In studies, the prevalence of migraine in cases with IBD was reported differently. The goal of this systematic review and meta-analysis was to estimate the pooled prevalence of migraine in IBD cases. Methods: Two researchers independently and systematically searched PubMed, Scopus, EMBASE, Web of Science, and google scholar. They also searched the gray literature including references of the included studies and conference abstracts which were published up to May 2021. Cross-sectional studies were included. Results: The literature search revealed 840 articles, and after deleting duplicates, 650 remained. For the meta-analysis, 10 studies were included. Totally, 62,554 patients were evaluated. The pooled prevalence of migraine in patients with IBD was 19% (95% CI: 15–22%). The pooled prevalence of migraine in ulcerative colitis (UC) was 10% (95% CI: 4–15%) (I 2 = 99.8%, P < 0.001). The pooled prevalence of migraine in the Crohn's disease (CD) group was 24% (95% CI: 17–30%) (I 2 = 98.8%, P < 0.001). The pooled odds of developing migraine in IBD cases was 1.51 (95% CI: 1–2.27) (I 2 = 90.8%, P < 0.001). Conclusions: The result of this systematic review and meta-analysis showed that the pooled prevalence of migraine in patients with IBD was 19% (95% CI: 15–22%).