This case report highlights the investigation and treatment of a 70‐year‐old male with cytomegalovirus (CMV) cholangiopathy. The patient underwent a kidney transplant in 2016 and presented 3 years later with the atypical presentation of left shoulder pain associated with dilated biliary tree and mild transaminitis. Initial endoscopic retrograde cholangiopancreatography (ERCP) showed diffuse stricture of the common bile duct, requiring stenting, and over the course of a year multiple stent changes were required to prevent cholestasis. CMV polymerase chain reaction (PCR) tests were conducted on bile duct brushings and found to be positive. Oral valganciclovir was given for 6 weeks but the strictures did not resolve. He underwent a laparoscopic total choledochectomy and hepaticojejunostomy as definitive treatment. CMV involvement of the biliary tract has rarely been reported in kidney transplant patients. Antiviral therapy in the form of ganciclovir or valganciclovir is often sufficient to eradicate CMV infection and improve clinical disease. Surgical management should be considered only if the patient has failed medical therapy, or if there is suspicion of malignancy. This case shows that in renal transplant patients presenting with cholangiopathy, CMV disease should be considered as a possible differential even in patients without early CMV infection or with prior CMV prophylaxis.