The modern management of gestational trophoblastic disease (GTD) has increased the cure rate more than 90%. Between 2 and 20% of patients presenting with metastatic GTD have liver involvement which has a poor prognosis with survival less than 40%. Very few cases have been documented in the literature of isolated liver metastasis in GTD. We present a rare case of GTD with only liver metastasis with heterotaxy syndrome with a great diagnostic dilemma. The patient was referred from a surgical oncologist of a private hospital with solitary liver tumor lesion and differential diagnosis of hepatocellular carcinoma. Incidental findings of unexplained raised β-hCG = 2 lakh lead to a differential diagnosis of GTN. There was a great diagnostic dilemma in diagnosis. β-hCG can be raised even in liver malignancies. It was difficult to explain large liver metastatic lesions without lung metastasis in GTN. Internal iliac ligation was done to stabilize the patient. After tumor board discussion, she received multi-agent chemotherapy and now on monthly follow-up. In women of childbearing age who present with hepatic masses, the possibility of choriocarcinoma should be as a differential diagnosis which is clinched by β-hCG estimation.