Choledochal cysts are a relatively rare congenital anomaly. Most cases are type I cysts according to the classification of Todani et al. Type II cysts, which resemble the diverticulum of the common duct, are extremely rare. Simple excision by laparoscopy is one of the safe surgery options for this type of cyst.We report the case of a 12-year-old boy with a type II choledochal cyst recognized during ultrasound investigation due to recurrent pain in the right upper abdomen. Magnetic resonance cholangiopancreatography (MRCP) confirmed the diagnosis and the cyst was excised laparoscopically. The postoperative course was uneventful, and the patient was discharged on the 3rd postoperative day. This report confirms the role of laparoscopic surgery in management of choledochal cysts in children and analyses the surgical options for type II choledochal cysts.Reports of type II choledochal cysts are very rare and standards of treatment are not yet clearly established. A simple excision may be sufficient and is associated with a low rate of complication. However, there is a risk of malignancy especially when any sign of metaplasia or dysplasia are observed in histopathological specimens.