During surgery for choledochal cyst (CC), any intrapancreatic CC (IPCC) must also be excised to prevent postoperative pancreatitis and stone formation. We report our technique for laparoscopic total IPCC excision (n = 16; mean age 6.0 years). We insert a fine ureteroscope with a light source into the opened CC through an extra 3.9-mm trocar placed in the epigastrium through a minute incision to identify the pancreatic duct orifice. By pulling the end of the ureteroscope emerging from the trocar gently to withdraw the tip from the pancreatic duct to where distal dissection was ceased under laparoscopic view, the IPCC can be measured. If longer than 5 mm, the distal CC is dissected further caudally until it is less than 5 mm. For accuracy, the distal CC is elevated with a suture that is exteriorized and clamped to provide constant traction. The IPCC was able to be measured in 11/16 (68 %). Initial lengths measured were 3-10 mm (5.2 ± 2.7 mm). Final IPCC were all 5 mm or less. Surgery was uncomplicated without any pancreatic duct injury and postoperative recovery was unremarkable. Follow-up MRI at 32 months showed no IPCC in any case. Measuring the IPCC enables total CC excision, thus reducing the potential for postoperative complications.