Perivascular epithelioid cell tumors (PEComas) are rare mesenchymal tumors. Unresectable malignant PEComas with TFE3 rearrangement have no recommended therapy to date. Here, we report the first case of malignant gastrointestinal PEComa with TFE3 rearrangement which has a response to the targeted therapy of an anti-VEGFR tyrosine kinase inhibitor (TKI), apatinib. A 31-year-old female was diagnosed with malignant gastrointestinal PEComa with TFE3 rearrangement and hepatic metastases. A resection of the giant retroperitoneal mass was performed. The patient received the anti-VEGFR TKI apatinib to treat the hepatic metastasis. The tumor remained stable during apatinib treatment and the progression-free survival (PFS) lasted about 7 months. This case suggests that targeting the VEGF/VEGFR signaling pathway may be an essential new therapeutic choice for TFE3-associated malignant PEComas.