Summary Background: Although studies have indicated that hyperthyroidism is associated with hypercoagulability, most such studies have focused only on examining the incidence of venous thrombosis. As far as we know, no study has attempted to explore the risk of pulmonary embolism (PE) among patients with hyperthyroidism. Objective: Using a nationwide population-based dataset, this study was aimed at estimating the risk of PE among hyperthyroidism patients during a 5-year period, as compared with non-hyperthyroidism patients during the same period. Methods: Data sourced from the Taiwan Longitudinal Health Insurance Database were analyzed. The study included 8903 patients with hyperthyroidism as a study cohort and 44 515 randomly selected patients without hyperthyroidism as a comparison cohort. Stratified Cox proportional hazard regressions were used to compute the 5-year PE-free survival rate between these two cohorts. Results: Of the total of 53 418 patients, 41 patients (0.08%) were identified as having PE during the follow-up period, 14 from the study cohort (0.16% of the hyperthyroidism patients) and 27 comparison patients (0.06% of patients from the comparison cohort). After adjustment for geographic region, monthly income, hypertension, diabetes, hyperlipidemia, peripheral vascular disease, coronary heart disease, cancer, recent surgery, recent fracture, pregnancy and the use of anticoagulants, the risk of having PE during the 5-year follow-up period was 2.31 times greater (95% confidence interval 1.20–4.45, P = 0.012) for patients with hyperthyroidism than for patients in the comparison cohort. Conclusion: We found an increased risk of PE in patients with hyperthyroidism. Clinicians should be aware of this increased risk.