Background: Patients with inflammatory bowel disease (IBD) are often accompanied by a more significant burden of depression or anxiety, and approximately one-third are prescribed antidepressants. However, previous studies on the efficacy of antidepressants in IBD have shown inconsistent results. Objectives: To evaluate the effect of antidepressants on depression, anxiety, disease activity, and quality of life (QoL) in IBD patients. Design: A systematic review and meta-analysis. Methods: We searched MEDLINE via Ovid, EMBASE via Ovid, the Cochrane Library, CINAHL, PsycINFO, Chinese CBM Database, China National Knowledge Infrastructure, VIP, and Wanfang Database from inception to 13th July 2022 without language restrictions. Results: In all, 13 studies containing 884 individuals were included. Compared with the control group, antidepressants were superior in reducing depression scores [standardized mean difference (SMD) = −0.791; 95% confidence interval (CI): −1.009 to −0.572; p < 0.001], anxiety scores (SMD = −0.877; 95% CI: −1.203 to −0.552; p < 0.001), and disease activity scores (SMD = −0.323; 95% CI: −0.500 to −0.145; p < 0.001). Antidepressants had a positive effect in reaching clinical remission [risk ratio (RR) = 1.383; 95% CI: 1.176–1.626; p < 0.001]. Higher physical QoL (SMD = 0.578; 95% CI: 0.025–1.130; p = 0.040), social QoL (SMD = 0.626; 95% CI: 0.073–1.180; p = 0.027), and Inflammatory Bowel Disease Questionnaire (SMD = 1.111; 95% CI: 0.710–1.512; p < 0.001) were found in the experimental group. No significant differences were observed in clinical response (RR = 1.014; 95% CI: 0.847–1.214; p = 0.881), psychological QoL (SMD = 0.399; 95% CI: −0.147 to 0.944; p = 0.152), and environmental QoL (SMD = 0.211; 95% CI: −0.331 to 0.753; p = 0.446). Conclusion: Antidepressants are effective for ameliorating depression, anxiety, disease activity, and QoL in IBD patients. Due to most studies having a small sample size, further well-designed studies are required.