Background Skull base chordomas (SBC) are rare malignant tumors and few factors have been found to be reliable markers for clinical decision making and survival prognostication. The aim of the present work was to identify specific prognostic factors potentially useful for the management of SBC patients. Methods A retrospective review of all the patients diagnosed and treated for SBC at the Fondazione IRCCS Istituto Neurologico “Carlo Besta” between January 1992 and December 2017 has been performed. Survival analysis was performed and a logistic regression model was used. Statistically significant predictors were rated based on their log odds in order to preliminarily build a personalized grading scale—the Peri-Operative Chordoma Scale (POCS). Results Fifty-nine primary chordoma patients were included. The average follow-up from the first treatment was 82.6 months (95% CI, 65.5–99.7). POCS was built over PFS and MR contrast enhancement (intense vs mild/no, value 4), preoperative motor deficit (yes vs no, value 3), and the development of any postoperative complications (yes vs no, value 2). POCS ranges between 0 and 9, with higher scores being associated with reduced likelihood of survival and progression-free state. Conclusions Our results show that preoperative clinical symptoms (motor deficits), surgical features (extent of tumor resection and surgeon’s experience), development of postoperative complications, and KPS decline represent significant prognostic factors. The degree of MR contrast enhancement significantly correlated to both OS and PFS. We also preliminarily developed the POCS as a prognostic grading scale which may help neurosurgeons in the personalized management of patients undergoing potential adjuvant therapies.