Pulmonary embolism (PE) is related to hypercoagulable status, such as malignancy, nature anticoagulant deficiency, pregnancy and use of estrogen replacement. It has rarely been reported to be associated with endocrine diseases. We presented a 32-year-old woman with combined Graves’ disease and PE. The initial presentation was progressive exertional dyspnea and cough for one month. First impression was Graves’ disease complicated with thyrotoxic crisis at the emergency department, but PE was suspected clinically. A dilemma of diagnostic process was the use of iodine-containing contrast media. Increasing iodine uptake of thyroid glands would lead to potential exacerbation of thyrotoxicosis, but PE is usually diagnosed with a contrast-enhancing computed tomography (CT) of chest. We demonstrated a good result of combined treatment for Graves’ disease with anti-thyroid drugs and submassive PE with catheter-directed thrombolysis and anticoagulants. After extensive literature review, we hypothesized that hyperthyroidism per se may contribute to the development of PE.