Intracranial mesenchymal chondrosarcoma (MCS) is a rare neoplasm. The diagnosis of MCS is confirmed by the presence of a biphasic pattern on histological examination, comprising undifferentiated small round cells admixed with islands of well-differentiated hyaline cartilage; however, a differential diagnosis may be challenging in some cases. A 28-year-old woman with a 2-month history of headache was referred to our hospital. Radiologic studies showed an extra-axial lobulated mass composed of calcified and uncalcified areas occupying the left middle fossa. Surgical resection was planned, but her headache suddenly worsened before her planned hospital admission and she was admitted as an emergency. Radiologic studies showed an acute hemorrhage in the uncalcified part of the mass. The mass was resected via the left zygomatic approach after embolization of the feeder vessels. The most likely histopathological diagnosis was MCS. However, the typical bimorphic pattern was not identified in our surgical samples; each undifferentiated area and well-differentiated area was observed separately in different tissue specimens, and no islands of well-differentiated hyaline cartilage were identified within the undifferentiated areas in the same specimen. Molecular assays confirmed the presence of HEY1-NCOA2 fusion. IRF2BP2-CDX1 fusion and IDH1/2 mutations were negative. The final diagnosis of MCS was made based on the presence of HEY1-NCOA2 gene fusion. MCS should be included in the differential diagnosis when radiologic studies show an extra-axial lobulated mass with calcification. Furthermore, molecular demonstration of HEY1-NCOA2 gene fusion may help make a precise diagnosis of MCS, especially in surgical samples lacking the typical histopathological features.