We describe a 27-year-old Japanese female with a recurrent nodule on the left big toe and local bone invasion. Histopathologically, the tumor consisted of nests of atypical cells with few mitotic cells, which partly formed gland-like structures. Areas of myxoid degeneration, positive for Alcian blue staining and that did not stain after they were digested with hyaluronidase, were prominent in the matrix among tumor cells. Positive staining was noted in tumor cells for cytokeratin (AE1+AE3), S-100 protein, neuron specific enolase (NSE), and glial fibrillary acidic protein (GFAP). These findings, especially positive GFAP staining were characteristic and very helpful for the diagnosis of the rare tumor—malignant chondroid syringoma. Based on the previous reports, 39% of cases were found to have metastatic lesions and 22% died of this malignant tumor. There have been no reports reporting effectiveness of chemotherapy and radiotherapy, and an early wide excision with a broad margin may be the most reliable treatment to date.