Blood type is reportedly correlated with the occurrence of cardiovascular diseases, presumably because of its effect on thrombogenicity. However, the relationship between blood type and thrombotic complications in atrial fibrillation (AF) remains unclear. This retrospective study analyzed the blood types of 1170 AF patients (mean age, 70 years; 58% men) who were followed up for up to 4 years. Patients with greater than mild mitral stenosis or prosthetic valves were excluded. The cohort included 305 (26%) type O, 413 (35%) type A, 333 (28%) type B, and 119 (10%) type AB patients. The primary endpoint of major adverse cerebrovascular events (MACE) occurred in 52 (4.4%) patients. When longitudinal outcomes were plotted, AB blood type patients had worse prognosis than non-AB blood type patients (p = 0.039), particularly type O blood patients (p = 0.049). Multivariate Cox regression analysis revealed that AB blood type was associated with higher MACE rates (adjusted hazard ratio, 2.01; 95% confidence interval, 1.01–4.00; p = 0.048) than non-AB blood types independent of anticoagulation therapy duration or CHA2DS2-VASc score. These indicate that AF patients with AB blood type are at an increased risk of MACE compared to those with non-AB blood type independent of the duration of anticoagulation or the CHA2DS2-VASc score.