The aim of this randomized controlled trial was to evaluate the efficacy of Unified Protocol (UP) for transdiagnostic treatment of psychological problems, such as anxiety, depression, and stress, and treating the intensity of gastrointestinal symptoms in individuals with Irritable Bowel Syndrome (IBS). Another aim of the study was to test whether emotion regulation mediates the effect of UP. Among 91 patients diagnosed with IBS (using ROME III criteria), 64 patients were eligible to participate in the study based on the inclusion/exclusion criteria. These patients were randomly assigned to either an intervention group (n = 32) that participated in 12 weekly UP treatment sessions or to a wait-list control group (n = 32). All patients completed the Depression, Anxiety, and Stress Scale (DASS-42), Emotion Regulation Questionnaire (ERQ), and Gastrointestinal Symptoms Rating Scale (GSRS) pre- and post-intervention. The data were analyzed with SPSS 20.0 software. The results of intention-to-treat (ITT) analysis indicated a significant decrease in depression, anxiety, stress, and gastrointestinal symptoms, as well as significant improvements in emotion regulation scores in the intervention group post intervention. All results were significant at P < .001. Mediation analyses indicated that changes in emotion regulation mediated the effect of UP on changes in emotional and gastrointestinal symptoms. UP was effective and influential in emotion regulation among the intervention group and caused a decline in emotional and gastrointestinal symptoms. Hence, this intervention is promising, but larger RCTs are needed to more investigate its efficacy. Future studies could also examine the efficacy of the UP in other medical conditions with co-occurring psychological conditions. The study is registered at the irct.ir database under registration number IRCT2017010431765N1. •Depression and anxiety are highly prevalent in patients with IBS.•Unified protocol (UP) was designed to improve emotional disorders concurrently.•Up improved the emotional and gastrointestinal symptoms individuals with IBS.•Emotion regulation mediated the effect of UP on emotional and gastrointestinal symptoms.•UP can be applied as a complementary treatment to other medical treatments for IBS.