Purpose One-anastomosis-gastric-bypass (OAGB) has become a common bariatric procedure worldwide. Marginal ulcers (MU) are a significant non-immediate complication of gastric bypass surgeries. There seems to be concern among surgeons that MU are more common after OAGB compared with Roux-en-Y gastric bypass (RYGB) due to the constant and extensive exposure of the anastomosis to bile. The aim of this study was to compare the incidence, presentation, and management of MU between the two surgeries. Materials and Methods A retrospective study of prospectively collected data was performed to include all consecutive patients between 2010 and 2020, who underwent elective OAGB or RYGB at our institution. Patients diagnosed with symptomatic MU were identified. Factors associated with this complication were assessed and compared between the two surgeries. Results Symptomatic MU were identified in 23/372 OAGB patients (6.2%) and 35/491 RYGB patients (7.1%) ( p  = 0.58). Time to ulcer diagnosis was shorter in OAGB patients (12 ± 11 vs. 22 ± 17 months, p  < 0.01). Epigastric pain was the common symptom (78% OAGB vs. 88.5% RYGB, p  = 0.7) and approximately 15% of ulcers presented with perforation upon admission (17% vs.11.4%, p  = 0.7). Re-operation was required in 5/23 OAGB (21.7%) and 6/36 RYGB (17%) patients ( p  = 0.11) while the rest of the patients were managed non-operatively. Conclusions The risk of developing a marginal ulcer is similar between patients who underwent OAGB and RYGB. Patients diagnosed with MU following OAGB tend to present earlier; however, the clinical presentation is similar to RYGB patients. The management of this serious complication seems to be associated with acceptable outcomes with comparable operative and non-operative approaches.