Background <p>Although Roux-en-Y gastric bypass (RYGB) has proven to be a safe and effective choice for long-standing weight loss, associated complications have been described. Among them, marginal ulcer (MU) has been recognized as one of the more significant postoperative complications. One-anastomosis gastric bypass (OAGB) has currently been the third most common procedure overall in the world. Similar to RYGB, concerns have emerged for MU risk after OAGB. This study aimed to compare the incidence of MU after RYGB versus OAGB.</p> Methods <p>This is a cross-sectional study that included 62 adult patients who underwent RYGB or OAGB and were followed up for a period of two years. The included patients underwent a complete general examination and upper gastrointestinal endoscopy.</p> Results <p>The prevalence of MU in RYGB patients was 19.4%, whereas in OAGB patients, it was markedly lower at 3.2%, with a statistically significant difference (<i>p</i> = 0.045). In the multivariate analysis, the presence of diabetes and the type of surgery (RYGB) were significant predictors for MU.</p> Conclusion <p>Marginal ulcers occurred at a relatively high rate after bypass surgery. OAGB demonstrated a significantly lower incidence of MUs compared to RYGB. Type 2 diabetes mellitus and the RYGB procedure were significant predictors of MU after adjusting for the confounding factors.</p>