Skull base chordoma is a rare and fatal disease, recurrence of which is inevitable, albeit variable. We aimed to investigate the clinicopathologic features of disease progression, identify prognostic factors, and construct a nomogram for predicting progression in individual patients. Data of 229 patients with skull base chordoma treated by one institution between 2005 and 2014 were retrieved and grouped as primary and recurrent. Kaplan-Meier survival of progression was estimated, taking competing risks into account. Multivariable Cox regression was used to investigate survival predictors. The primary group consisted by 183 cases, gained more benefits on 5-year progression-free survival (PFS) (51%) and mean PFS time (66.9months) than the recurrent group (46 cases), in which 5-year postrecurrent PFS was 14%, and mean postrecurrent PFS time was 29.5months. In the primary group, visual deficits, pathological subtypes, extent of bone invasion, preoperative Karnofsky performance scale (KPS) score, and variation in perioperative KPS were identified as independent predictors of PFS. A nomogram to predict 3-year and 5-year PFS consisted of these factors, was well calibrated and had good discriminative ability (adjusted Harrell C statistic, 0.68). In the recurrent group, marginal resection (P = 0.018) and adjuvant radiotherapy (P = 0.043) were verified as protective factors associated with postrecurrent PFS. Factors for tumor progression demonstrated some differences between primary and recurrent cases. The nomogram appears useful for risk stratification of tumor progression in primary cases. Further studies will be necessary to identify the rapid-growth histopathological subtype as an independent predictor of rapid progression.