Skull base chordoma (SBC) is a rare and refractory tumor with a high rate of relapse. We aimed to investigate the relationships between different treatment measures and progression-free survival (PFS) outcomes. Data from 234 SBC patients from one institution were retrieved from a prospectively maintained database. After grouping, the clinicopathological features and mean estimated PFS times were subject to inter-group and intra-group comparisons, and prognostic factors of PFS were estimated by statistical analyses. Two typical primary patients who suffered from repeated tumor relapses are described. In addition to pathological subtype (p = 0.005), the initial treatment measure for the primary cases (n = 180) was identified as an independent factor of tumor progression (p = 0.002). The patients with gross total resection exhibited the best mean estimated PFS time (109.5 months). Patients with intralesional resection exhibited the shortest PFS time (38.3 months), with an almost significant difference (p = 0.058) compared to those with adjuvant radiotherapy following intralesional resection (56.6 months). For the recurrent group (n = 54), marginal resection (p = 0.007) and adjuvant radiotherapy (p = 0.041) were confirmed as independent protective factors for PFS. The longest mean PFS time (60.3 months) was noted in those patients who received marginal resection followed by adjuvant radiotherapy. Treatment measures were crucial for post-surgical tumor progression in both primary and recurrent cases. For primary cases, gross total resection and adjuvant radiotherapy offered more PFS benefits to all patients and those who underwent intralesional resection. Marginal resection and adjuvant radiotherapy, which are proposed as a general treatment paradigm for primary tumors, were also equally effective when applied to relapsing tumors.