INTRODUCTION AND IMPORTANCE: Biliary hamartomas are uncommon, benign anomalies of the intrahepatic bile ducts, typically asymptomatic and identified incidentally during imaging or surgery. Although malignant transformation into cholangiocarcinoma is exceptionally rare, it presents considerable diagnostic and therapeutic challenges. Prompt recognition is essential to guide appropriate surgical intervention and improve patient outcomes. CASE PRESENTATION: We report the case of a 52-year-old woman, a nonsmoker and non-alcoholic, who presented with progressive abdominal distension and pain for one month. She had no prior history of liver disease, viral hepatitis, parasitic infections, intrahepatic stones, cholangitis, autoimmune diseases or abdominal trauma. On clinical examination, a palpable mass was noted in the right hypochondriac region. Laboratory investigations revealed hypoalbuminemia (1.4 g/dL) (not due to liver cirrhosis, as clinical and imaging findings excluded it), elevated liver enzymes (ALT 78 U/L, AST 67 U/L, GGT 67 U/L, ALP 330 U/L), and an elevated CA19-9 level (65 U/mL), with otherwise normal hematological and tumor marker profiles. Imaging studies demonstrated a 10 × 7 cm multilocular cystic lesion in the left liver lobe without evidence of vascular or nodal involvement. A preoperative diagnosis of cholangiocarcinoma or intraductal papillary neoplasm of the bile duct (IPNB) was considered. Liver biopsy revealed biliary hamartoma. Due to the lesion's size and malignant suspicion, laparoscopic left hepatectomy with regional lymphadenectomy was performed. CLINICAL DISCUSSION: Compared to previously reported 35 cases (mean age 69.7 year, male predominance), our patient was a younger female with a tumor in the left lobe. The case was managed laparoscopically, and was initially suspected as IPNB, adding unique diagnostic and management insights. Histopathological examination confirmed cholangiocarcinoma arising from a biliary hamartoma. Immunohistochemistry showed positivity for CK-19 and p53, supporting the diagnosis. The normalization of CA19-9 levels postoperatively and absence of recurrence at 6 months follow-up support successful surgical management. This case illustrates the uncommon risk of malignant transformation in biliary hamartomas and emphasizes the need for thorough diagnostic assessment and prompt surgical management. CONCLUSION: While biliary hamartomas are generally benign, the rare possibility of their progression to cholangiocarcinoma should be carefully considered, particularly when imaging reveals atypical features or tumor markers are elevated. In such scenarios, surgical resection remains the definitive treatment with promising prognostic outcomes.