To compare 5-year gastroesophageal reflux outcomes following Laparoscopic Vertical Sleeve Gastrectomy (LVSG) and Laparoscopic Roux-en-Y gastric bypass (LRYGB) based on high quality randomized controlled trials (RCTs). We conducted a sub-analysis of our systematic review and meta-analysis of RCTs of primary LVSG and LRYGB procedures in adults for 5-year post-operative complications (PROSPERO CRD42018112054). Electronic databases were searched from January 2015 to July 2021 for publications meeting inclusion criteria. The Hartung-Knapp-Sidik-Jonkman random effects model was utilized to estimate weighted mean differences where meta-analysis was possible. Bias and certainty of evidence was assessed using the Cochrane Risk of Bias Tool 2 and GRADE. Four RCTs were included (LVSG n = 266, LRYGB n = 259). An increase in adverse GERD outcomes were observed at 5 years postoperatively in LVSG compared to LRYGB in all outcomes considered: Overall worsened GERD, including the development de novo GERD, occurred more commonly following LVSG compared to LRYGB (OR 5.34, 95% CI 1.67 to 17.05; p = 0.02; I2 = 0%; (Moderate level of certainty); Reoperations to treat severe GERD (OR 7.22, 95% CI 0.82 to 63.63; p = 0.06; I2 = 0%; High level of certainty) and non-surgical management for worsened GERD (OR 3.42, 95% CI 1.16 to 10.05; p = 0.04; I2 = 0%; Low level of certainty) was more common in LVSG patients. LVSG is associated with the development and worsening of GERD symptoms compared to LRYGB at 5 years postoperatively leading to either introduction/increased pharmacological requirement or further surgical treatment. Appropriate patient/surgical selection is critical to minimize these postoperative risks.