Infected liver cysts may have a unique etiology and require further workup. Generally, large cyst is easy to be symptomatic. In contrast, smaller cyst with infection in our case is associated with ampullar cancer of Vater without typical manifestations of jaundice, body weight loss, and pancreatitis. We presented the case of a 61-year-old man with infected liver cysts, which is confirmed by abdominal computer tomography and liver cysts drainage with bacterial culture. Endoscopic retrograde cholangiopancreatography revealed a swollen papilla of Vater and a dilated common bile duct. Biopsy confirmed adenocarcinoma of the ampulla of Vater. Further surgical pathology revealed communication of bile duct with liver cysts and no evidence of tumor invasion to pancreatic duct and common bile duct. The infected liver cysts may result from ascending cholangitis which is secondary to ampullar cancer. The patient underwent the Whipple procedure, unroofing of the right-side liver cyst, and partial hepatectomy without complications. There is no recurrence of infected liver cyst and cancer till now after follow-up for 3 years. Infected liver cysts are rarely associated with ampullar cancer. Early diagnosis and successful resection of early stage ampullary neoplasm ensure favorable outcomes.