A 45-year-old man was suffering from abdominal pain and vomiting. He was admitted to our hospital with a diagnosis of ileus and obstructive jaundice. He had undergone Roux-en-Y anastomosis for choledocholithiasis 14 years earlier. A computed tomography scan revealed a dilated afferent loop and dilated intrahepatic bile duct. Upper gastrointestinal examination with contrast medium and percutaneous transhepatic cholangiography showed a high intestinal obstruction around the jejunojejunal anastomosis. The patient underwent laparotomy based on a diagnosis of obstructive jaundice due to ileus. During the operation, he was found to have internal herniation of the small bowel through a rent in the mesentery around the Roux-en-Y anastomosis for choledochojejunostomy. The hernia was reduced, and bowel resection was performed due to stenosis of the afferent loop. Jejunojejunal anastomosis was re-performed and the defect in the mesocolon was closed. Internal herniation after Roux-en-Y anastomosis is a rare sequela, but it should be recognized that this complication can occur after Roux-en-Y anastomosis. For prevention of internal herniation around the Roux-en-Y limb, secure closing of the mesenteric defects is important.