Background: Patients with hyperthyroidism have higher risk of atrial fibrillation (AF). However, the risk of thromboembolic event in patients with hyperthyroidism-related AF is controversial. Objectives: The aim of the study was to examine the risk of thromboembolic events in AF patients with/without hyperthyroidism. Methods: The national retrospective cohort study enrolled AF population was derived from the Taiwan National Health Insurance Research Database. The comparison between the AF patients with clinical hyperthyroidism (HT-AF group) and AF patients without hyperthyroidism (nonthyroid AF group) was made in a propensity score matched cohort and in a real-world setting, of which, the CHA2DS2-VASc level was treated as a stratum variable. The outcomes were ischemic stroke and systemic thromboembolism. Results: There were 3,880 patients in HT AF group and 178,711 in non-thyroid AF group. After propensity score analysis, the incidence of thromboembolism event and ischemic stroke were lower in HT AF patients than non-thyroid AF patients (1.6 versus 2.2 events per 100 personyears; HR, 0.73; 95% CI, 0.64-0.82 and 1.4 versus 1.8 events per 100 person-years; HR, 0.74; 95% CI, 0.64-0.84, respectively) in the 4.3 ± 3.2 year follow up period. The differences persistently existed in those receiving anticoagulants or not. In AF patients without anticoagulants, the incidence densities of ischemic stroke/systemic thromboembolism were significantly lower in HT AF group than those in non-thyroid AF group at CHA2DS2-VASc scores = 4 (HR, 0.41; 95% CI, 0.35-0.48, p < 0.001), while the differences disappeared in case of score = 5 (HR, 0.80; 95% CI, 0.63-1.02, p = 0.071). Conclusion: Patients with HT AF had lower incidence of thromboembolic events as compared to non-thyroid AF patients. The threshold of CHA2DS2-VASc score for anticoagulation in AF patients with clinical hyperthyroidism should be further evaluated. Highlights • The incidence of thromboembolic event was different between hyperthyroidism-related atrial fibrillation (HT-AF) and non-thyroid AF patients. • Hyperthyroidism did not confer additional risk of thromboembolic event at CHA2DS2-VASc of = 4. • The benefit of anticoagulation strategy in patients with hyperthyroidism-related AF should be further evaluated, especially at low CHA2DS2-VASc score. [ABSTRACT FROM AUTHOR]