A 42-year-old woman underwent abdominal ultrasonography during her annual medical checkup and a mass in her left flank region was identified. She was admitted to the hospital for further examination. A computed tomography scan and endoscopic examination revealed a submucosal tumor in the wall of the descending colon. Systemic magnetic resonance imaging and positron emission tomography scans did not show any other lesions. The lesion was suspected to be a colonic GIST and left hemicolectomy was performed. Upon macroscopic examination, the tumor was 5 cm in the greatest dimension, well-circumscribed but uncapsulated, and extended from the muscular propria into the subserosa. The cut surface was hemorrhagic and necrotic. Microscopically, the tumor cells consisted of spindle and epithelioid cells with a granular cytoplasm. Based on the clinical diagnosis of GIST, a panel of immunohistochemistry including KIT, PDGFRα, discovered on GIST-1 (DOG1), CD34, S100, desmin, and Ki67 were performed. The tumor cells were positive for PDGFRα and negative for KIT, DOG1, CD34, S100, and desmin. The Ki-67 index was 3%. We initially suspected the tumor to be a PDGFRα-positive GIST. Mutational analysis did not reveal any mutation in PDGFRα or KIT, and suggested the possibility of a low-grade tumor other than GIST. Upon further examination, the tumor cells were found to be positive for HMB45 and calponin, and negative for melanA, MITF, SOX10, and actin. These results were compatible with PEComa. This tumor was immunohistochemically negative for TFE3, but did not show rearrangement of TFE3 in fluorescence in situ hybridization (FISH) (data not shown). The patient was alive without recurrence 5 months after the resection.