Perivascular epithelioid cell tumors (PEComas) are rare mesenchymal tumors with widespread distribution throughout the body and unpredictable clinical behavior. Recently, a subset of these tumors has been reported to harbor Transcription Factor E3 (TFE3) gene rearrangement with distinct morphologic and immunophenotypic features. Although limited, these tumors may represent a separate entity from the conventional PEComas and may require different treatment approaches. Surgery is the main treatment option with no clear consensus on systemic therapy. Here, we present the first case of a malignant pediatric colonic TFE3-associated PEComa with isolated liver metastasis leading to liver transplantation for the local control.