Treatment of common bile duct (CBD) stones after Roux-en-Y gastric bypass (RYGB) poses a particular challenge given the altered anatomy and inability to perform a standard endoscopic retrograde cholangiogram (ERC). The optimal treatment strategy for intraoperatively encountered CBD stones in post-RYGB patients has not been established. To compare outcomes following laparoscopic transcystic common bile duct exploration (LTCBDE) and laparoscopy-assisted transgastric ERC for CBDs during cholecystectomy in RYGB-operated patients. Swedish nationwide multi-registry study. The Swedish Registry for Gallstone Surgery and ERCs, GallRiks (n = 215,670), and the Scandinavian Obesity Surgery Registry (SOReg) (n = 60,479) were cross-matched for cholecystectomies with intraoperatively encountered CBD stones in patients with previous RYGB surgery between 2011 and 2020. Registry cross-matching found 550 patients. Both LTCBDE (n = 132) and transgastric ERC (n = 145) were comparable in terms of low rates of intraoperative adverse events (1% versus 2%) and postoperative adverse events within 30 days (16% versus 18%). LTCBDE required significantly shorter operating time (P = .005) by on average 31 minutes, 95% confidence interval (CI) [10.3-52.6], and was more often used for smaller stones <4 mm in size (30% versus 17%, P = .010). However, transgastric ERC was more often used in acute surgery (78% versus 63%, P = .006) and for larger stones >8 mm in size (25% versus 8%, P < .001). LTCBDE and transgastric ERC have similarly low complication rates for clearance of intraoperatively encountered CBD stones in RYGB-operated patients, but LTCBDE is faster while transgastric ERC is more often used in conjunction with larger bile duct stones.