Background: Perivascular epithelioid cell tumors (PEComas) are very rare mesenchymal neoplasms, and have been found in various organs such as the liver, kidney, falciform ligament, uterus, uterine cervix, and both the small and large bowel. However, only 3 cases of mesenteric PEComa have been described in the literature so far. The treatment and prognosis of malignant mesenteric PEComas are discussed. Case Report: We report the case of a 59-year-old man diagnosed with PEComa. He underwent segmental resection of the jejunum and tumor resection. Malignant mesenteric PEComa was confirmed on the basis of clinicopathological features. Tumor resection was followed by concurrent chemoradiotherapy. Conclusion: Besides surgery, no effective treatment for malignant PEComa has been established thus far because of the rarity of this tumor. Here, we report our experience of treating a malignant mesenteric PEComa using surgery and subsequent adjuvant therapy, which effectively controlled disease progression and prevented local recurrence.