We report a case of perivascular epithelioid cell tumor (PEComa) with an SFPQ/PSF-TFE3 gene fusion in a 14-year-old girl treated for adrenal neuroblastoma for 4 years. Imaging studies revealed a tumor in the wall of the sigmoid colon, which was radiologically different from the neuroblastoma, together with several inguinal and cervical lymph node metastases of the neuroblastoma. Microscopically, the tumor in the sigmoid colon showed sheet-like growth of epithelioid cells with abundant clear cytoplasm and round nuclei, which were separated by thin fibrovascular septa. These epithelioid cells were immunohistochemically positive for vimentin, gp100 (detected with monoclonal antibody HMB-45), and TFE3, and the tumor was diagnosed as PEComa. In a fluorescence in situ hybridization assay using an in-house probe for TFE3, the tumor cells showed split signals, indicating a rearrangement of TFE3. Molecular cloning using 5' rapid amplification of complementary DNA ends and subsequent reverse transcription-polymerase chain reaction revealed an SFPQ/PSF-TFE3 gene fusion. To the best of our knowledge, this is the second reported case of metachronous PEComa subsequent to a primary tumor, and the first report confirming an SFPQ/PSF-TFE3 gene fusion in PEComa.