We describe the laparoscopic treatment of a patient presenting with congenital choledochal cyst. Our patient was a 19-year-old man with a complaint of recurrent abdominal pain due to pancreatitis. The choledochal cyst was type I and had a common channel of pancreatobiliary duct, as revealed by endoscopic retrograde cholangiopancreatography. Under laparoscopic guidance, the dilated bile duct and the gallbladder were excised, and a Roux-en-Y anastomosis was constructed with an endo-EEA. Finally, end-to-side anastomosis was carried out by the continuous suture method, aided by an Endostitch between the stump of the hepatic duct and the Roux-en-Y limb. After the operation, slight hyperamylasemia was observed for several days but further treatment was not necessary. Postoperative symptoms were minimal, and the patient was discharged on the 11th day after the procedure. Although it is difficult and time-consuming, laparoscopic operation is highly beneficial for the patient. The use of such instruments as the endostapler and Endostitch may help to simplify this complex intracorporeal procedure involving division and anastomosis of the digestive tract.