Retroperitoneal chordomas are exceedingly rare and account for less than 5% of all primary bone malignancies. Their etiology remains unknown. We report a rare case of an extravertebral chordoma of the retroperitoneum in a 71-year-old man treated with surgical resection and post-operative spot-scanning proton beam therapy. We describe how to safely treat a retroperitoneal target to a prescription dose over 70 Gy (relative biological effectiveness) with spot-scanning proton beam therapy and also report a dosimetric comparison of spot-scanning proton beam therapy versus intensity-modulated radiation therapy. This case not only highlights a rare diagnosis of an extravertebral retroperitoneal chordoma but it also draws attention to the dosimetric advantages of proton beam therapy and illustrates a promising radiotherapeutic option for retroperitoneal targets.