INTRODUCTION: Perivascular epithelioid cell neoplasms (PEComas) are a rare type of mesenchymal tumor that can be found in various visceral and soft tissues in the body. Approximately fifty cases have been reported in the gastrointestinal (GI) tract. Typically, management of these lesions is laparoscopic or open surgical resection followed by chemotherapy if there is metastatic disease. The majority of GI PEComas are benign, colonic masses in middle-aged females. This case describes a malignant, colonic PEComa in a 16-year-old male. To the best of our knowledge, this is the largest malignant, colonic PEComa in an adolescent, and this is the first case to demonstrate successful endoscopic mucosal resection (EMR) of a PEComa. CASE DESCRIPTION/METHODS: A 16-year-old male with history of IgA vasculitis during childhood presented with acute onset of bilious emesis in the setting of severe, intermittent, left lower quadrant abdominal pain and constipation for one month. Lab testing was unremarkable. Computed tomography revealed a non-obstructing, nodular mass in the transverse colon. The patient underwent colonoscopy, during which the 6-cm large, semi-sessile, broad-based polyp was removed by piecemeal EMR. EMR was technically challenging due to the size, broad base, and location of the mass. Histology of the tissue showed a predominance of fascicular spindled cells, scattered areas with epithelioid morphology, and prominent vasculature, consistent with a PEComa. The tissue stained positive for HMB-45, MART-1, and cathepsin. Based on the size (>5 cm), nuclear atypia, and high mitotic activity, the lesion was defined as malignant. Though the lesion was removed to the submucosa, there was concern for deeper extension, so he underwent laparoscopic transverse colectomy with primary anastomosis. Pathology confirmed there was not any residual tumor in the resected colon or metastasis to lymph nodes. Positron emission tomography did not show metastasis. Fifteen months have elapsed and the patient has not had recurrence on imaging. DISCUSSION: There are few cases of GI PEComas. This case demonstrates a rare presentation of a large, malignant GI PEComa in a young male and is the first case of successful endoscopic removal of a malignant PEComa. The surgical specimen revealed no evidence of residual PEComa, and the patient has not had evidence of recurrence on imaging, verifying successful removal of his PEComa. This supports the notion that EMR should be considered for definitive management in patients with these lesions.