Background: Functional gastrointestinal disorders such as irritable bowel syndrome (IBS) report clinical improvement following probiotic therapy, but whether psychiatric comorbidity and quality-of-life in IBS improves directly or in directly is unknown. This meta-analysis synthesized the evidence regarding the effects of probiotics on quality of life (QoL), anxiety and depression in IBS. Methods: The review was executed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines using the databases PubMed, Web of Science and Cochrane Library. For QoL, the data were meta-analyzed, and for anxiety and depression a qualitative analysis was performed. Results: Thirty-five placebo-controlled studies were included of which 11 were eligible for meta-analysis. QoL improved with probiotic and placebo similarly, with the probiotic interventions slightly superior (mean QoL difference—0.36 (95% CI: 0.07, 0.64); p = 0.01). Anxiety and depression were similar between placebo and probiotic groups following therapy. Conclusion: For IBS, probiotic therapy improved QoL, but had no effects on anxiety and depression. However, the applied probiotics were not developed for selective effects on psyche and the brain. Therefore, it remains to be shown whether or not patients with IBS would benefit from second generation probiotics developed for these central effects (psychobiotics).