Background: The prevalence of comorbid depression is high in chronic gastrointestinal disorders, including irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). For these two disorders in particular, the findings have not been consistent. This meta-analysis systematically compares the rates and severity of comorbid depression between IBS and IBD patients. Methods: A systematic literature search was conducted using PubMed, PsycINFO, Embase, Cochrane Library, Wan Fang, SinoMed, Chinese National Knowledge Infrastructure from their inception date to September 12, 2017 for comparative studies on IBS and IBD patients. Standardized mean differences (SMDs) and odds ratios (OR) of comorbid depression were calculated using random effect models. Data on comorbid anxiety in the included studies were also extracted and analyzed. Results: Altogether, 22 studies with 1,244 IBS and 1,048 IBD patients were included. While there was no significant group difference in the prevalence of depression (10 studies, OR = 1.18, 95%CI: 0.87–1.60, P = 0.29), the IBS group had more severe depression (pooled SMD = 0.18, 95%CI: 0.04–0.33, P = 0.01) and anxiety than the IBD group (pooled SMD = 0.31, 95%CI: 0.14–0.49, P = 0.0006). Sixteen (72.7%) studies were assessed as ‘high quality’ using the Newcastle–Ottawa Scale (NOS). Conclusions: Although the prevalence of comorbid depression was similar between groups, IBS patients had more severe comorbid depressive and anxiety symptoms compared to IBD patients. Appropriate assessment and treatment of depressive and anxiety symptoms in these patient groups should be implemented.