Xanthogranulomatous inflammation is a rare inflammatory reaction, characterized by lipid-laden macrophages, known as xanthomas, in histopathologic examination. Aggressive xanthogranulomatous inflammation often manifests as local infiltration but does not affect distant organs unless combined with rare systemic diseases. We report a case of focal xanthogranulomatous pyelonephritis (XGP) associated with severe xanthogranulomatous cholecystitis. Focal XGP was suspected in radiologic examination that showed a cystic lesion with an infiltrative margin, which were surgically resected and confirmed in pathologic examination. To our knowledge, this is the first report of focal xanthogranulomatous pyelonephritis associated with xanthogranulomatous cholecystitis. Moreover, we found peripheral hypointensity around the cystic lesion in the T2-weighted image, probably reflecting hemorrhage and fibrosis of the xanthogranulomatous inflammation.