Aim Pouchitis is a clinically significant complication of ileal pouch–anal anastomosis with its prevalence varying in the literature. Pouchitis is thought to occur more commonly in patients with ulcerative colitis (UC) than in patients with familial adenomatous polyposis (FAP). We conducted a systematic review with meta‐analysis of all published literature to report the prevalence of pouchitis in all pouch patients as well as specifically in UC and FAP. We also investigated the prevalence of acute and chronic pouchitis in UC and FAP. Methods A meta‐analysis was conducted by searching the Embase, Embase Classic and PubMed databases between 1978 and 2021 exploring the prevalence of pouchitis in UC and FAP. We then performed a random effects model in order to find the pooled prevalence of pouchitis and used odds ratios to report differences in the prevalence of pouchitis in UC and FAP. Results Fifty‐nine full papers and conference s were included in the meta‐analysis comprising 18 117 patients with UC and 860 with FAP. The prevalence of pouchitis in UC was 0.32 (95% CI 0.27–0.37) and in FAP was found to be 0.06 (95% CI 0.03–0.15). The odds ratio of pouchitis in UC patients compared with FAP patients was 4.95 (95% CI 3.17–7.72, P < 0.0001). Conclusions Our findings support the consensus that the prevalence of pouchitis is higher in UC than in FAP. More significantly our findings suggest that the true prevalence of pouchitis is higher than commonly reported in the literature. This literature may help counsel patients prior to undergoing restorative proctocolectomy.