Background: Perivascular epithelioid cell tumors (PEComas) of the skull base are extremely rare. Here we report the first description of a malignant PEComa mimicking jugular foramen schwannoma and presenting as Collet-Sicard syndrome, and we review the previous literature on PEComas of the head, neck and skull base. Case description: A 29-year-old woman presented with hoarseness, dysphagia, vomiting, and headache. She was first diagnosed with Collet-Sicard syndrome caused by thrombosis of the sigmoid and transverse sinuses. She was treated with anticoagulant therapy, and the hoarseness and paralysis of the accessory nerve improved. Later, at age 31, the hoarseness again worsened. At another hospital, enhanced computed tomography revealed a tumor in the jugular foramen extending to the neck and medially displacing the internal carotid artery. She was referred to our hospital for further examination and was diagnosed with jugular foramen schwannoma causing thrombosis of the sinuses. At the one-year follow-up, the tumor had grown rapidly and had started to surround the internal carotid artery. We therefore performed a tissue biopsy of the tumor in the jugular foramen and neck. Based on pathological analysis, we made a definitive diagnosis of malignant PEComa. Conclusions: It may be extremely challenging to reach an accurate diagnosis of PEComa in the skull-base region, which can cause a delay in treatment initiation. When atypical clinical features for a skull-base tumor are found, we recommend preliminary biopsy to obtain a definitive diagnosis and initiate an appropriate treatment strategy as early as possible.