This study reported treatment outcomes of proton or photon adjuvant therapy for chordomas of the skull base and spine. Data of 424 patients from the National Cancer Database was included for analysis. For all chordoma cases, and for all cases of skull base chordoma, this study found no difference in OS between the photon and proton groups. However, a significant OS benefit with proton over photon was reached (p = 0.012) in patients with spine chordomas.