Thymomas are rare tumors of the mediastinum; a limited number of small studies have evaluated the outcomes in these patients. We identified 668 patients with thymoma from the Swedish Cancer Registry, and 2,719 population-based matched controls. We obtained information on autoimmunity from the nationwide inpatient/outpatient hospital discharge Registry. We constructed Kaplan-Meier curves for survival analysis, conditional regression and Cox proportional hazards models to evaluate the association between thymoma and autoimmune diseases, and standardized incidence ratios (SIRs) to evaluate the risk for second cancers following thymoma. Compared with controls, patients with benign or malignant thymoma had a poorer (p < 0.001) 5-year (79%, 53% vs. 91%), 10-year (65%, 39% vs. 78%) and 20-year (43%, 18% vs. 55%) overall survival. For thymoma patients, younger age at diagnosis and being diagnosed in recent years were associated with a better survival. Compared with controls, thymoma patients were more likely to have an autoimmune disease at some point during their lives (32.7% vs. 2.4%, respectively, p < 0.001), most frequently myasthenia gravis (24.5%), systemic lupus erythematosus (2.4%) and red cell aplasia (1.2%). Thymoma patients had twofold excess risk for second cancers compared with the general population, most notably: non-melanoma skin cancer (SIR = 10.6, 95% confidence intervals (CI) = 6.0-17.3), non-Hodgkin lymphoma (SIR = 6.8, 95% CI = 3.00-13.0), and cervical (SIR = 6.9, 95% CI = 1.4-20.1), endocrine (SIR = 4.7, 95% CI = 1.3-12.0), and prostate cancer (SIR = 3.0, 95% CI = 1.7-4.8). Despite the improved survival for thymoma patients over time, they have worse survival than controls. Thymoma patients are in need for follow-up to detect and manage autoimmune diseases and cancer.