Despite an increase in our understanding of the pathophysiology of irritable bowel syndrome (IBS), in the context of abnormal gut-brain axis communication, and advances in both pharmacological and non-pharmacological treatment of the disorder, there remain areas in which there are misconceptions and controversies in the clinical management of IBS. This Perspective aims to highlight some of the most common misconceptions and controversies in IBS management, including those that the scientific literature has resolved, but for which further education of clinicians dealing with patients with IBS might be required to implement the findings from medical research. Areas of remaining contention are also discussed, as are suggestions as to how these issues could be addressed, both by advances in clinical practice and by further research.