This study aimed to analyze the surgical outcomes for recurrent thymic epithelial tumors and identify the factors associated with post-recurrence survival, using an updated Japanese nationwide database. The cohort that developed recurrence after the initial resection was extracted from an updated database of patients whose thymic epithelial tumors were treated surgically between 1991 and 2010. Furthermore, we reviewed clinicopathological and prognostic factors of re-resected cases. Post-recurrence survival outcomes and cause-specific deaths in non-re-resected cases were also reviewed. We enrolled 191 patients who underwent re-resection and 259 patients who did not. In the surgery group, more patients with early-stage disease, less aggressive World Health Organization (WHO) histological classification, initial complete resection, and shorter recurrence-free intervals were included. Non-thymic carcinoma, absence of preoperative treatment, longer recurrent-free interval, single-site recurrence, and R0-1 re-resection were all significantly favourable prognostic factors for post-recurrence survival in the surgery group, according to univariable analyses. Non-thymic carcinoma histology, longer recurrence-free interval, and R0-1 re-resection were identified as independent prognostic factors according to multivariable analysis. The post-recurrence survival of the entire cohort with R2 re-resection was significantly better than that of the non-surgery group, although it was not demonstrated that patients with thymoma who underwent R2 re-resection had significantly better post-recurrence and lower cause-specific death. R0-1 re-resection was newly identified as a prognostic factor after re-resection, in addition to non-thymic carcinoma histological classification and longer recurrence-free intervals, as documented in the initial report.