Background and objective: Endoscopic retrograde cholangiopancreatography (ERCP) is the gold standard for managing malignant biliary obstruction (MBO), but it is challenging in patients with surgically altered anatomy (SAA). EUS-guided hepaticogastrostomy (EUS-HGS) and enteroscopy-assisted ERCP are alternative techniques, but their comparative efficacy and safety in this population are not well-researched. Herein, we evaluated the outcomes of EUS-HGS versus single-balloon–assisted enteroscopy ERCP (SBE-ERCP) in MBO patients with SAA. Patients and methods: This retrospective study included 70 patients with MBO who underwent EUS-HGS (n = 29) or SBE-ERCP (n = 41) at a single center between April 2015 and June 2024. Data on the patient characteristics, procedure details, time to recurrent biliary obstruction (TRBO), and adverse events (AEs) were analyzed. Results: The EUS-HGS group showed a higher technical success rate (100% vs. 68%, P = 0.002), shorter procedure time (23 vs. 50 min, P < 0.001), and longer TRBO (251 vs. 103 d, P = 0.020) as compared with the SBE-ERCP group. Subgroup analysis revealed that pancreatobiliary cancer and SBE-ERCP were significantly associated with a shorter TRBO. When stratified by stent type, the median TRBO in the SBE-ERCP with PS group was 49 days, serving as the reference. In comparison, the median TRBO was 140 days in the SBE-ERCP with the self-expandable metallic stent group (hazard ratio [HR], 0.46; P = 0.181), 127 days in the EUS-HGS with PS group (HR, 0.38; P = 0.055), and 701 days in the EUS-HGS with the self-expandable metallic stent group (HR, 0.13; P = 0.014). The overall incidence of AEs was comparable between the 2 groups (20.6% vs. 17.1%), and there were no severe AEs. Regarding reintervention, there was no significant difference in technical success rate and procedure time between EUS-HGS and SBE-ERCP. Conclusion: EUS-HGS was associated with a superior technical success rate, shorter procedure time, and longer stent patency, without an increased risk of AEs, as compared with SBE-ERCP. Thus, EUS-HGS should be appropriate for managing MBO patients with SAA.