The cause of jejunojejunal intussusception, a rare complication after Roux-en-Y gastric surgery, remains unclear. Here, we present a case of retrograde jejunojejunal intussusception that occurred after laparoscopic distal gastrectomy with Roux-en-Y reconstruction. A 51-year-old woman who had undergone laparoscopic distal gastrectomy and Roux-en-Y reconstruction for early gastric cancer 6 years previously was admitted to our hospital with abdominal pain. Abdominal CT revealed the "target sign," and she was diagnosed as having small bowel intussusception. Laparoscopic surgery resulted in a diagnosis of retrograde intussusception of the distal jejunum of the Roux-en-Y anastomosis with retrograde peristalsis in the same area. The Roux-en-Y anastomosis site and intussuscepted segment were resected laparoscopically. To the best of our knowledge, this is the first report of laparoscopic diagnosis of retrograde peristalsis in the distal jejunum of a Roux-en-Y anastomosis. Additionally, relevant published reports concerning this unusual condition are discussed.