A choledochal cyst is a rare condition that requires surgical treatment to prevent complications, such as obstructive jaundice, cyst rupture, cholangitis, and the risk of malignancy. Complete cyst excision is considered the best option, as it reduces the risk of inflammation and the development of cholangiocarcinoma. Therefore, cholecystectomy and complete cyst resection followed by reconstruction with a Roux-en-Y hepaticojejunostomy is the treatment of choice. We present a case (with video) that shows the complete resection of a type I choledochal cyst with Roux-en-Y reconstruction of two separate ducts since the right posterior duct reached the cyst independently. The laparoscopic approach offers all the advantages of mini-invasive surgery and better visualization of the structures; however, biliary reconstruction to fine ducts implies a surgical challenge that requires high training in mini-invasive surgery.