Crohn’s disease of the duodenum is an uncommon condition. Our case was an extremely rare manifestation of Crohn’s disease, who presented with obstruction of the pylorus and the first and the second parts of the duodenum. Because of the severity of the obstruction, he underwent laparoscopic pancreaticoduodenectomy. Postoperative pancreatic leakage and bowel fistula were not observed, and there was no morbidity during the follow-up period. There was also no disturbance in digestive function, postoperatively. This is the first case employing laparoscopic pancreaticoduodenectomy to cure benign lesions leading to duodenal obstruction. Minimally invasive laparoscopic pancreaticoduodenectomy technology shows a very big advantage in treating this rare benign Crohn’s disease.