Irritable bowel syndrome (IBS) is a common disorder requiring complex, multidisciplinary management. Antidepressants are commonly used and recommended in guidelines for the treatment of patients with IBS. We assessed randomized controlled trials (RCTs) on antidepressants in patients with IBS, with specific attention to study design and data quality/reporting characteristics. Following a comprehensive search, data and RCT characteristics were systematically summarized. Fragility index, representing the number of positive “events” that the study relies on for its significance, was calculated. Eighteen RCTs were included. Overall, tricyclic antidepressants (TCAs), but not selective serotonin reuptake inhibitors (SSRIs), appeared to be efficacious in IBS. Eight studies reported on adverse events (AEs), which were significantly greater in patients receiving antidepressants versus placebo. The median (mean) fragility index of TCA trials was 0 (1.5). RCTs with positive results had significantly lower placebo rates (20.8%) versus negative studies (45.7%; p < 0.0001). RCTs exhibited limitations related to study design (sample size and blinding), data analysis (outcomes and placebo response), and data reporting (selective reporting of AEs and publication bias). Careful consideration of limitations of RCTs on antidepressants in IBS is warranted to formulate a safe and beneficial treatment regimen for patients with IBS.