Endoscopic biliary drainage for malignant biliary obstruction (MBO) in patients with surgically altered anatomy is challenging, and technical difficulty could differ by the anatomy. Balloon endoscopy-assisted endoscopic retrograde cholangiopancreatography (BE-ERCP) and endoscopic ultrasonography-guided biliary drainage (EUS-BD) are both emerging procedures, and we conducted the single-center, retrospective study to compare clinical outcomes of BE-ERCP and EUS-BD for MBO. Consecutive patients with surgically altered anatomy who underwent BE-ERCP or EUS-BD for MBO were retrospectively studies. Technical and clinical success rates, adverse events (AEs), and time to recurrent biliary obstruction (TRBO) were compared. Patient characteristics were comparable between BE-ERCP (n = 118) and EUS-BD (n = 32), other than more patients with hepaticojejunostomy in the BE-ERCP group (66% vs. 44%, P = 0.03). Technical success rate was significantly higher in the EUS-BD group (70% vs. 94%, P = 0.005), but clinical success rates (84% vs. 90%, P = 0.55), early AE (14% vs. 22%, P = 0.29) and late AE rates (42% vs. 38%, P = 0.84), and RBO rates (31% vs. 34%, P = 0.67) were comparable between the groups. TRBO was 170 and 206days in the BE-ERCP and EUS-BD group (P = 0.37). In the subgroup analysis of patients with the intact papilla, the technical success rate of BE-ERCP was as low as 55%, compared to 94% in EUS-BD (P = 0.003). EUS-BD was associated with higher technical success rate than BE-ERCP for MBO in patients with surgically altered anatomy.