Background Recent evidence suggests that exposures in early life that are known to influence microbiome development may affect the risk of developing inflammatory bowel disease (IBD). Cesarean section has been associated with altered colonization of commensal gut flora and is thought to predispose to immune-mediated diseases later in life. Aims To evaluate the risk of IBD, Crohn’s Disease (CD), and Ulcerative Colitis (UC) according to mode of delivery (C-section vs vaginal delivery). Methods A systematic search was performed in PubMed and Embase. The primary outcome was the risk of IBD in individuals delivered vaginally compared to those born by C-section. Secondary outcomes were UC and CD risk according to mode of delivery and IBD risk in individuals born by emergent compared to elective C-section. Publication bias was evaluated by funnel plots and Egger’s test. Study’s quality was characterized using the Newcastle–Ottawa Scale. Results Ten studies fulfilled the inclusion criteria, of which seven were population-based. No publication bias was detected. Overall, 14.164 IBD patients and 4.206.763 controls were included. Being born by C-section was not associated with increased risk of IBD OR 1.01, 95% CI (0.81–1.27), p  = 0.92, CD OR 1.15, 95% CI (0.94–1.42), p  = 0.18 or UC OR 0.94, 95% CI (0.61–1.45), p  = 0.79. No differences were found between emergent and elective C-section in IBD OR 1.05, 95% CI (0.59–1,87), p  = 0.87. Substantial heterogeneity was found in statistical analysis, and further studies are needed. Conclusion Overall, the risk of developing IBD was not affected by mode of delivery.