Laparoscopic choledochal cyst excision and hepaticojejunostomy for choledochal in children is performed only at particular institutions because of the technical difficulty. Although choledochal cyst excision and hepaticojejunostomy are feasible, the small working space of infants makes intraabdominal Roux-Y reconstruction technically challenging. A 2-month-old girl diagnosed with a choledochal cyst underwent complete laparoscopic choledochal cyst excision and hepaticojejunostomy, including intraabdominal Roux-Y reconstruction with a 5-mm stapler. After cyst excision, Roux-Y reconstruction was performed in the intraabdominal cavity. Jejunojejunostomy was performed in a side-to-side fashion using a 5-mm stapler, and the entry hole was closed laparoscopically by hand-sewing, along with the mesentery defect. All procedures were performed by laparoscopic surgery. The postoperative course was uneventful, and the patient showed a quick recovery. Using small-diameter instruments, completely laparoscopic procedures for choledochal cyst are feasible.