Treatment of choledocholithiasis after Roux-en-Y gastric bypass (RYGB) is a therapeutic challenge given the altered anatomy. To overcome this technical difficulty, different modified endoscopic approaches have been described but significant morbidity accompanies these procedures. The aim of the present study is to report our experience with laparoscopic transcystic common bile duct exploration (LTCBDE) as treatment of choledocholithiasis after RYGB. This is a retrospective cohort study of 854 consecutive patients with RYGB at a single institution between January 2007 and December 2019. Our study population focused on patients who developed biliary events after RYGB. Demographic data and perioperative parameters were compared between patients who underwent laparoscopic cholecystectomy (LC) after RYGB with (defined as Group A) and without (defined as Group B) LTCBDE. Fifty-seven (8.93%) patients developed a biliary event after RYGB that led to LC. Of those, 11 (19.2%) presented choledocholithiasis during intraoperative cholangiogram and were simultaneously treated with LTCBDE (Group A). Choledocholithiasis was unsuspected in the preoperative setting in 7 (63.6%) of the 11 patients. The procedure was successful in 90.9% (n = 10). Comparing Group A and B, no statistically significant differences were found regarding age, gender, length of hospital stay, and morbidity (p > 0.05). Mean operative time of Group A was 113.1 min, adding, on average, 35 min to LC (113.1 min vs 77.9 min, p = 0.004). LTCBDE offers an effective approach for common bile duct stones in patients who underwent RYGB. This procedure did not add significant length of hospital stay nor morbidity to laparoscopic cholecystectomy.