Background: Inflammatory complications including chronic refractory pouchitis and Crohn's disease (CD)-like complications of the pouch are common complications after ileal pouch-anal anastomosis (IPAA) following colectomy for ulcerative colitis (UC). We performed a systematic review and meta-analysis to evaluate the efficacy of anti-TNF therapy in distinguishing patients with chronic refractory pouchitis from those with CD-like complications of the pouch. Methods: We performed a systematic literature search to identify articles and abstracts reporting anti-TNF agents efficacy in treating inflammatory complications of the pouch after IPAA for UC. Short-term and long-term remissions were evaluated at 8 weeks 95% CI[5-10] and 12 months 95% CI[12-18.5], respectively. Results: We identified 21 articles and 3 abstracts including 313 patients treated either with infliximab (n = 194) or adalimumab (n = 119) for inflammatory complications of the pouch. The rates of short-term and long-term clinical remission were 0.50 (95% CI [0.37-0.63]; I-2 = 0.57) and 0.52 (95% CI[0.39-0.65]; I-2 = 0.59), respectively. The rate of remission after anti-TNF induction therapy seemed to be higher in CD-like complications of the pouch 0.64 (95% CI[0.5-0.77]; I-2 = 0.18), compared to refractory pouchitis 0.10 (95% CI [0.00-0.35]; I-2 = 0.00) (P = 0.06), whereas no such difference appeared after long-term maintenance therapy 0.57 (95% CI[0.43-0.71]; I-2 = 0.32) and 0.37 (95% CI [0.14-0.62]; I-2 = 0.47), respectively (P = 0.57). Sensitivity analyses suggested no difference in outcomes. No significant publication bias has been detected. Conclusion: Anti-TNF agents have a clear trend to have higher and faster efficacy in CD-like complications of the pouch compared to refractory pouchitis, highlighting the need to differentiate these two entities both in daily practice and clinical trials.