Background <p>Roux-en-Y gastric bypass (RYGB) has long been established as one of the most efficient therapeutic options for patients with obesity and associated medical conditions. However, the impact of concurrent vagal transection during pouch creation on postoperative outcomes remains underreported.</p> Methods <p>This retrospective cohort study examined patients who underwent RYGB between January 2011 and December 2023, with 1 to 5 years of follow-up. Patients were stratified into two groups: vagal sparing RYGB (VS) and non-vagal sparing RYGB (NVS). Data collected included postoperative complications, intraoperative characteristics, weight trajectories, resolution of obesity-related medical conditions, and mortality. Statistical analysis methods included paired t-tests, multivariate regression, and Cox regression models.</p> Results <p>Out of 1521 patients, 374 (24.6%) underwent VS-RYGB and 1147 (75.4%) had NVS-RYGB. Patients were predominantly female (80.8%), with a mean age of 47.6 ± 12.1 years and body mass index (BMI) of 46.0 ± 7.7 kg/m². NVS had significantly longer operative times (<i>p</i> &lt; 0.001) and a higher lysis of adhesions rate (<i>p</i> &lt; 0.001). Marginal ulcer rate was also significantly higher in NVS compared to VS (<i>p</i> = 0.03). In contrast, the rate of dumping syndrome (<i>p</i> = 0.13) and cholelithiasis (<i>p</i> = 0.65) was not significantly different between groups. While overall weight outcomes were similar, VS reached maximum percentage of total weight loss (%TWL) earlier (<i>p</i> = 0.02). Both groups showed comparable obesity-related condition outcomes.</p> Conclusion <p>NVS-RYGB was associated with higher operative time. Additionally, vagal transection was significantly associated with marginal ulcer occurrence. Our findings support the potential advantage of vagal-sparing RYGB.</p> Graphical Abstract <p></p>