Irritable bowel syndrome (IBS) is common in adolescents with a pronounced negative impact on quality of life. A pattern of avoidance behavior is commonly seen in the IBS population, which is associated with more gastrointestinal (GI) symptoms. Exposure-based cognitive behavior therapy (CBT) targets the avoidance behavior to reduce symptoms, but it is unknown whether reduced avoidance is a mediator of symptom improvement in adolescent IBS. Stress has been suggested to play a key role in worsening GI symptoms and is also a potential mediator of the treatment effect in IBS. This study was based on data from a randomized controlled trial (N = 101) that evaluated exposure-based internet-delivered CBT (Internet-CBT) compared with a wait-list for adolescents with IBS. We investigated whether avoidance behavior and perceived stress mediated the improvement in global GI symptoms due to treatment. We found that a change in avoidance behavior, but not perceived stress, mediated the effect of exposure-based Internet-CBT on GI symptoms. The decrease in avoidance behavior explained a large portion (67%) of the total treatment effect. Moreover, a unidirectional relationship over time was observed between avoidance behavior and GI symptoms. Our conclusion is that exposure-based CBT in adolescent IBS reduces avoidance and, consequently, reduces GI symptoms.