Inflammatory myofibroblastic tumor (IMT) of the biliary tree is extremely rare and is generally a benign condition, though malignant change is possible. Making a differential diagnosis between this lesion and other malignant conditions is very difficult on preoperative imaging studies. Hence, the final diagnosis of IMT may be made during or after operation depending on the pathologic examination. We treated a 63-year-old woman who received right hepatectomy with caudate lobectomy under the suspicion of hilar cholangiocarcinoma. Frozen biopsy during the operation showed carcinoma in situ and there were stromal cells in the bile duct's resection margins. The postoperative hospital course was uneventful except for minor bile leakage. At postoperative month 4, she developed jaundice, ascites and pleural effusion. Computed tomography images showed a mass-like lesion in the porta hepatis with portal vein thrombosis and a right chest wall mass. Excisional biopsy was done and the pathology report was malignant spindle cell tumor suggestive of an aggressive form of IMT. Her condition rapidly deteriorated regardless of the best supportive care and she expired at postoperative month 5. Further investigation is necessary to clarify the reasons for recurrence and infiltration of this disease.