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BACKGROUND: Modulating gut microbiota is a potential treatment for irritable bowel syndrome (IBS). This meta-analysis explored whether fecal microbiota transplantation (FMT) is successful in treating IBS. METHODS: A systematic review was performed to find trials on FMT in IBS. Ratios and relative ratios (RR) of improvement for single-arm trials (SATs) and randomized controlled trials (RCTs) were calculated, respectively. Changes in IBS Severity Scoring System (IBS-SSS) and IBS Quality of Life (IBS-QOL) instrument compared to baseline in FMT versus placebo groups were pooled. RESULTS: In SATs, 59.5% (95% confidence interval (CI) 49.1-69.3) of IBS patients showed significant improvement. In RCTs, there were no differences between FMT and control in improvement (RR=0.93 (95% CI 0.50-1.75)) or changes in the IBS-SSS and IBS-QOL. CONCLUSIONS: FMT was not effective in IBS. Variations in FMT methods and patient factors may contribute to the heterogeneous results of the trials.