A 55-year-old woman presented to hospital with epigastric pain and jaundice. Diagnostic imaging studies revealed a biliary stricture of the hepatic confluence and a hepatic tumour of the left and caudate lobes with a portal tumour thrombus, which occupied the main portal trunk, the umbilical portion of the left portal vein, and the right anterior and posterior portal branches. Left hepatic trisegmentectomy, caudate lobectomy, portal tumour thrombectomy, bile duct resection and bilioenteric anastomosis were performed. There were no other lesions, and so it was diagnosed as a primary lymphoma of the liver (B-cell, diffuse, large cell type). The patient underwent postoperative chemotherapy and has remained well for 4.5 years after surgery. Primary lymphoma of the liver is very rare, and this is the first case report with bile duct invasion and tumoral occlusion of the portal vein.