A 49-year-old man without heart murmur was admitted with fever because of bacteremia following a tooth extraction. Antibiotics rapidly alleviated the fever; however, a small nodule in the pulmonary artery was identified on computed tomography (CT). When the patient experienced chest discomfort with fever, CT demonstrated the absence of the nodule and the appearance of an abnormal lung opacity, and echocardiography showed turbulent retrograde flow in the pulmonary artery. We had the rare opportunity to follow a case of pulmonary bacterial endarteritis and subsequent pulmonary embolism with clinically silent patent ductus arteriosus (PDA) that was confirmed by 3-dimensional CT.