Background: We aimed to compare the effectiveness of mindfulness-based stress reduction and compassion-focused on the cognitive regulation of emotion in patients with irritable bowel syndrome (IBS). The research method was the semi-experimental type, with pre-test, post-test, follow-up, and experimental and control groups. Methods: The population included patients with IBS in Isfahan city; 45 of them were selected by convenience sampling method and randomly assigned to 3 groups (15 in each group). Then, the patients of one experimental group received eight sessions of 90 minutes of a mindfulness-based stress reduction program, while the other experimental group received eight sessions of 90 minutes of compassion-focused therapy. The measurement tools included the Cognitive Emotion Regulation Questionnaire (Garnefski and Kraaij, 2002) and a short clinical interview. Research data were analyzed using variance analysis with repeated measures on one factor (mixed design). Results: Both intervention methods were equally effective in changing the cognitive regulation of adaptive emotion mean scores (P<0.01), but the effect of compassion-focused therapy on improving the mean scores of cognitive regulation of adaptive emotion was more than mindfulness-based stress reduction therapy (P<0.05). Conclusion: It was concluded that both intervention methods can be used as complementary treatment for patients with IBS.