Bacterial endocarditis is a disease that is difficult to diagnose early and difficult to treat. According to the literature, it may occur in patients with congenital heart valve disease and repaired valves. This report describes an eight-year-old boy with a history of ventricular septal defect (VSD). The patient came to our hospital and complained of repeated fever after root canal treatment of the upper left primary first molar. After blood bacteria culture and echocardiogram examination, he was diagnosed with bacterial endocarditis. After six weeks of antibiotics and dental treatment, there were no bacteria detected in the blood. The vegetation on the heart valve atrophied and no clinical fever was found before discharge. Oral health care and regular dental examination can reduce oral bacterial infection and prevent bacterial endocarditis.