Ectopic hepatocellular carcinoma (HCC) is rare and there has been no report on ectopic HCC arising from both the bile duct and the gallbladder. It is difficult to establish a correct diagnosis for this kind of HCC based on preoperative imaging. All of the preoperative imaging examinations misdiagnosed the HCC as cholangiocarcinoma in our case. However, via retrospective analysis of this case, we found that the patient was positive for hepatitis virus markers and that a tumor marker (α-fetoprotein) was significantly elevated. Therefore, diagnosis of HCC with significantly elevated α-fetoprotein (>200 μg/L) is highly likely, particularly with chronic hepatitis and excluding pregnancy and tumor of genital system.