BACKGROUND: Different techniques are used to create a gastrojejunal anastomosis (GJ) in laparoscopic Roux-en-Y gastric bypass (LRYGB). This study compares long-term weight loss and technique-related morbidity between circular (CSA) GJ and linear (LSA) stapled GJ. METHODS: The clinical data of LRYGB patients prospectively registered in a database were retrospectively analyzed. The primary endpoints were long-term excess weight loss (EWL) and excess BMI loss (EBL). The risk factors were adjusted via propensity score matching (PSM), and the long-term morbidity rates of the procedures were compared as time-to-event-data using hazard ratios (HR). RESULTS: Two hundred forty-three patients underwent surgery between 2012 and 2014 (CSA n = 109; LSA n = 134). No significant differences in weight development were shown during 6 years postoperatively between CSA and LSA. A mixed effects regression analysis before and after PSM revealed that CSA performed better than LSA after 6 years (potentially biased by low follow-up rates for this period). CSA was associated with higher overall morbidity (LSA 26.1% vs. CSA 38.8%, HR = 1.58, p = 0.048), incisional hernia (LSA 0.7% vs. CSA 6.4%, HR = 10.0, p = 0.006), and GJ stenosis rates (LSA 0% vs. CSA 17.4%, p < 0.001). LSA was associated with marginal ulcers (LSA 8.2% vs. CSA 0.9%, HR = 5.5, p = 0.012). CONCLUSIONS: Marginal ulcers have been linked to LSA, while CSA has been associated with higher rates of overall morbidity, stenosis of the GJ, and incisional hernia. No difference terms of weight loss were observed between the CSA and LSA groups during the initial six postoperative years. After 6 years, CSA may offer benefits in terms of sustained weight loss; however, the clinical relevance of these differences appears minimal.