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Bile duct tumor thrombus (BDTT) is an uncommon finding in hepatocellular carcinoma (HCC), potentially mimicking cholangiocarcinoma (CCA). Recent studies have suggested that HCC with BDTT could represent a prognostic factor. We report the case of a 47-year-old male patient admitted to the University Hospital of Bari with abdominal pain. Blood tests revealed the presence of an untreated hepatitis B virus infection (HBV), with normal liver function and without jaundice. Abdominal ultrasonography revealed a cirrhotic liver with a segmental dilatation of the third bile duct segment, confirmed by a CT scan and liver MRI, which also identified a heterologous mass. No other focal hepatic lesions were identified. A percutaneous ultrasound-guided needle biopsy was then performed, detecting a moderately differentiated HCC. Finally, the patient underwent a third hepatic segmentectomy, and the histopathological analysis confirmed the endobiliary localization of HCC. Subsequently, the patient experienced a nodular recurrence in the fourth hepatic segment, which was treated with ultrasound-guided percutaneous radiofrequency ablation (RFA). This case shows that HCC with BDTT can mimic different types of tumors. It also indicates the value of an early multidisciplinary patient assessment to obtain an accurate diagnosis of HCC with BDTT, which may have prognostic value that has not been recognized until now.