<italic>Background</italic>. Failure factors in reaching the blind end (papillae of Vater, bilioenteric anastomosis) during short-type single-balloon enteroscope-assisted endoscopic retrograde cholangiopancreatography (sSBE-assisted ERCP) in patients with Roux-en-Y (R-Y) reconstruction remain to be evaluated. <italic>Aims</italic>. We investigated the failure factors in such patients. <italic>Methods</italic>. We retrospectively studied 253 initial sessions of sSBE-assisted ERCP at three endoscopy centers from April 2008 through September 2017, examining failure factors and complications associated with scope insertion in patients with R-Y reconstruction. <italic>Results</italic>. R-Y reconstruction was performed in 157 patients (with gastrectomy: 122 patients; without gastrectomy plus bilioenteric anastomosis: 35 patients). R-Y without gastrectomy (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mn>0.001</mml:mn></mml:math>; odds ratio (OR), 5.73; 95% confidence interval (CI), 2.07 to 16.01) and the presence of peritoneal dissemination (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M2"><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mn>0.021</mml:mn></mml:math>; OR, 4.71; 95% CI, 1.27 to 17.54) were significant failure factors. Insufficient sSBE length was the cause of failure in 17 (11%) of the 157 patients, and 13 (76%) of the 17 patients were with R-Y without gastrectomy. In cases of insufficient short-type length, using a long-type SBE significantly increased the success rate (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M3"><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mn>0.002</mml:mn></mml:math>). Gastrointestinal stenosis was a significant failure factor (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M4"><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mn>0.011</mml:mn></mml:math>) in patients with peritoneal dissemination. Perforation occurred in 2 patients who responded to conservative treatment. <italic>Conclusions</italic>. Failure factors during sSBE-assisted ERCP were R-Y without gastrectomy and the presence of peritoneal dissemination.