The family of PEComa encompasses a heterogeneous group of related mesenchymal neoplasms with myomelanocytic differentiation, a distinctive subset of which is characterized by TFE3 gene rearrangement. Recurrent YAP1::TFE3 fusion has been found in clear cell stromal tumor of the lung (CCST-L), and most recently, in two cases classified as inflammatory spindle cell PEComa. However, the potential relationship between CCST-L and PEComa remains unclear. Herein, we report a case of primary pulmonary malignant TFE3-rearranged PEComa with prototypical morphological and immunohistochemical features, unexpectedly harboring YAP1::TFE3 fusion. Our findings further expanded the morphological and molecular spectrum of PEComa-like mesenchymal neoplasms of the lung.