Conventional duodenoscopy is challenging to perform in patients with a surgically altered anatomy (SAA). Short single-balloon enteroscopy (SBE) is an innovative alternative. We investigated the performance of short SBE in patients with SAA and explored risk factors for unsuccessful intubation. Patients who underwent short SBE from October 2019 to October 2023 were retrospectively analyzed. Successful enteroscopic intubation was defined as the endoscope reaching the papilla of Vater, the pancreaticobiliary-enteric anastomosis, or the target site of the afferent limb. In total, 99 short SBE procedures were performed in 64 patients (40 men, 24 women) with a mean age of 61 years (range, 36–86 years). The patients had a history of choledochoduodenostomy (
n
= 1), Billroth II gastrojejunostomy (
n
= 11), pancreaticoduodenectomy (
n
= 17), Roux-en-Y reconstruction with hepaticojejunostomy (
n
= 31), and Roux-en-Y reconstruction with total gastrectomy (
n
= 4). Successful enteroscopic intubation occurred in 32 of 64 (50.0%) patients, and in 57 of 99 (57.6%) procedures. No perforation or severe pancreatitis occurred. Multivariable analysis showed that Roux-en-Y reconstruction was a risk factor for intubation failure (hazard ratio, 4.2; 95% confidence interval, 1.1–15.8;
p
= 0.033). Short SBE is efficacious and safe in patients with postsurgical anatomy. Roux-en-Y reconstruction adversely affects the success of short SBE intubation.