Primary biliary melanoma arises from proliferating melanocytes in the mucosal surface of the bile duct and is extremely rare. Since the vast majority of biliary melanomas represent metastases of cutaneous origin, accurate preoperative diagnosis of melanoma and exclusion of other primary sources are vital in cases involving primary lesions. Although melanomas with pigmented cells have typical signal characteristics, obtaining a non-invasive pre-treatment diagnosis remains difficult, due to their low incidence. Here, the case of a 61-year-old male Asian patient who presented with upper quadrant abdominal pain, swelling and jaundice for 2 weeks, and who was diagnosed with primary biliary melanoma following extensive preoperative blood analyses, computed tomography (CT) and magnetic resonance imaging (MRI), is described. Post-resection immunohistochemistry confirmed the diagnosis and the patient received six chemotherapy cycles of temozolomide and cisplatin, however, progression of multiple liver metastases was observed at the 18-month follow-up CT. The patient continued with pembrolizumab and died 17 months later. The present case of primary biliary melanoma is the first reported diagnosis based on typical MRI features and the exhaustive exclusion of a separate primary origin.