The patent foramen ovale (PFO) is known as a risk of paradoxical embolism in patients with deep venous thromboses. However, PFO is usually found after systemic embolic symptoms become apparent. A 60-year-old male had complained of dyspnea for two weeks. Ultrasound echocardiography showed a thrombus straddling PFO, and venous echography showed blood clots in the right popliteal and soleus veins. Contrast computed tomography revealed multiple pulmonary embolisms and a thrombus in the right atrium expanding to the left atrium through the atrial septum. The straddling thrombus in the atrium and pulmonary thrombi were extirpated under circulatory arrest with deep hypothermia. An inferior vena cava filter was inserted intravenously four days after surgery. The patient was discharged on the 19th postoperative day without any signs of thromboembolism. Prompt surgery is considered important to prevent thromboembolism in the case of impending paradoxical embolism.