The primary treatment for chordoma is en-bloc resection (removal of the tumor in one piece). En-bloc resection is usually not possible with skull based tumors because of their location.  Is essential that a team of experienced surgeons remove the tumor.

Surgery may be combined with radiation before or after the surgery to improve the chance of a successful outcome.

With the exception of poorly differentiated and dedifferentiated chordoma, chemotherapy does not have a role in treating primary chordoma tumors. Some studies have indicated that targeted chemotherapy agents may have a role in slowing the disease progression in recurrent and metastatic chordoma. Research is currently underway to develop more effective chemotherapy agents.