Background: Germinal centers (GCs) can be observed in the thymic tissues of individuals with thymomaassociated myasthenia gravis (TAMG). This study aimed to investigate the association between the presence of GCs in the thymus and the clinical outcomes of patients with TAMG following thymoma resection. Methods: A retrospective review was conducted on patients diagnosed with TAMG who underwent surgical removal of the thymoma. Upon reviewing thymic tissue slides to determine the presence of GCs, patients were divided into GC-positive and GC-negative groups. The association between the presence of GCs and the achievement of minimal manifestation (MM) or pharmacological remission (PR) was analyzed after adjusting for clinical characteristics. Results: Of the 111 patients, 41 (36.9%) with thymic follicular hyperplasia were classified into the GC-positive group, and the remaining patients were classified into the GC-negative group. Initial analyses including the entire patient cohort did not demonstrate a significant association between GC and achieving MM or PR postthymectomy. However, a refined analysis that excluded patients treated with prednisolone before thymectomy revealed a significantly lower cumulative incidence of MM in the GC-positive group (p = 0.011). The presence of GCs was negatively associated with achieving MM, even after adjusting for confounding variables (hazard ratio = 0.479, 95% confidence interval = 0.237-0.968, p = 0.040). Conclusion: Ectopic GCs in the thymus may serve as a prognostic factor for poor outcomes in patients with TAMG. Further research is needed to elucidate the role of GCs in the pathogenesis of TAMG and predict clinical outcomes following treatment.