A 26-year-old man with chronic granulomatous disease complicated by multiple liver abscess was admitted to our hospital for hepatic resection and allogeneic bone marrow transplantation (BMT) from an HLA-matched sibling. We diagnosed the patient with Aspergillus liver abscesses based on computed tomographic findings, elevated serum levels of beta-D-glucan, positive test for galactomannan antigen, and the findings of laboratory cultures. Since the liver abscess could not be treated by drainage and administration of antifungals, we resected the posterior segments of the liver, which contained the abscess (S1, S6). However, abscess recurred in the remaining part of the liver 1 month later. The patient received allogeneic BMT from an HLA-matched sibling. During BMT, we continuously administered liposomal amphotericin B (L-AMB) via the hepatic artery (25 mg/day) to treat the liver abscess. There were no adverse effects during hepatic arterial infusion of L-AMB, and the liver abscess disappeared after BMT. These results suggest that hepatic arterial infusion of L-AMB is effective in treating fungal abscess in the liver.