Gallbladder agenesis is a rare congenital anomaly of the biliary tract, due to failure of the gallbladder and cystic duct budding off of the common bile duct during fetal development. Cholangiocarcinoma (CCA) is a malignant tumor arising from the biliary ducts in patients with underlying chronic biliary tract inflammation, primary sclerosing cholangitis, or other diseases. Although few studies have reported cases of cholelithiasis in patients with congenital gallbladder agenesis, there is only one other known case of concomitant cholangiocarcinoma and congenital gallbladder agenesis. Herein we present a case of recurrent gallstones in a male, diagnosed with gallbladder agenesis intraoperatively and with pathology consistent with cholangiocarcinoma.