The incidence of cysts of the biliary system is approximately 1 in 100,000 to 150,000 in Western populations. The pathophysiology of biliary tree cysts is believed to be a result of an anomalous pancreaticobiliary junction. Although surgery is the preferred treatment for biliary tree cysts, surgical resection of the cyst does not eliminate the risk of malignancy, but rather it reduces the risk. The main goal of surgery is complete resection of the cyst and reconstruction of the biliary tree. In addition to the complexity of the procedure, variations of the biliary tree and the hepatic hilum luminal structures make the surgery more difficult for the surgeon. In this report, the case of a 46-year-old male patient is described. He presented at the clinic with a previously diagnosed choledocal cyst of Todani class 1 and a history of peptic ulcer perforation surgery. Further evaluation verified a choledocal cyst measuring 6x4 cm. Robotic complete surgical resection of the cyst and reconstruction of the biliary tree with hepaticojejunostomy was performed. During the bladder dissection, a luminal structure localized near Calot's triangle was observed and determined to be the left hepatic artery coursing over the anteromedial gall bladder and entering the liver at the level of the bladder fundus. The cyst and gall bladder were dissected while preserving the left hepatic artery. In conclusion, a minimally invasive approach for choledocal cyst resection should be performed at experienced centers because of frequent variations in both the hepatic arterial system and the biliary tract.