Background Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder characterised by chronic abdominal pain and altered bowel habits. However, IBS is often associated with a variety of comorbidities, and the causal relationship between IBS and oral ulcers is currently unclear.Methods A Two-sample Mendelian randomization study was used to investigate the relationship between irritable bowel syndrome and oral ulcers, with Cochran's Q test testing for heterogeneity between instrumental variables (IV). Horizontal pleiotropy was tested by MR-Egger regression intercept analysis and MR-PRESSO analysis.Results MR analysis revealed a significant causal relationship between irritable bowel syndrome and increased risk of developing oral ulcers for IVW (OR = 1.023, 95% CI: 1.007–1.040; p = 0.003). Similar results were observed in the weighted median (OR = 1.022, 95% CI: 1.003–1.042; p = 0.018). Sensitivity analyses and Cochran's Q test did not reveal the presence of pleiotropy and heterogeneity.Conclusions The present study suggests that oral ulcers may be a complication of irritable bowel syndrome and the results have important clinical implications, however, the biological mechanisms of this association need to be further explored.