Backgroud Misdiagnosis and missed diagnosis of septic pulmonary embolism (SPE), a, rare disease, occurs among, the patients with right heart infective endocarditis. The purpose of this study was to analyze the characteristics of SPE and improve the early diagnosis and treatment. Methods We retrospectively studied 34 patients with septic pulmonary embolism caused by right-sided infective endocarditis who were seen from June 1, 2002 to June 1, 2013. We reviewed the medical records and radiological images of these cases and extracted the following information: age, gender, and symptoms, physical examination, laboratory findings, transthoracic echocardiography (TTE) results, treatment information, comorbid medical conditions, and outcomes. Microbiological samples were collected and processed according to well-established and published guidelines. Results We identified basic heart disease in 97.1% of the patients. A high proportion of the right-sided infective endocarditis patients had congenital heart defects (82.4%); predominantly, ventricular septal defects. Clinical symptoms were fever (97.1%), cardiac murmurs (94.1%) and fatigue (88.2%). Respiratory symptoms included cough (58.8%), pleuritic chest pain (47.1%) and hyoxemia (52.9%). Positive blood cultures were grown from 35.2% of patients and 50.0% were caused by staphylococcal species. Chest X-rays or CT examinations detected patchy infiltrates and/or nodules in all cases. Transthoracic echocardiography demonstrated infectious foci of the right-side heart in all cases. Parenteral antibiotics were administered for all, and cardiac surgery was carried out for 76.5% of patients with an effective rate of 82.3%. Conclusions SPE lacks characteristic clinical manifestation. Congenital heart disease is a common risk of SPE. Most patients with SPE have a good prognosis as long as early diagnosis and proper treatment can be provided.