Inflammatory pseudotumor of the liver is a rare benign lesion that can mimic a malignant liver neoplasm. A case of inflammatory pseudotumor of the liver found in association with a malignant gastrointestinal stromal tumor (GIST) of the small bowel was reported. The inflammatory pseudotumor was misdiagnosed as a metastasis from the GIST by frozen section. A correct diagnosis was made only after histopathological examination of the paraffin section of the resected specimen. This case is particularly interesting because of the association of the two rare pathological entities and the diagnostic dilemma that arose from the similarity of their histological appearances. To our knowledge, this association has not been reported in the literature.