The mortality rate associated with cerebral hemorrhage as a complication of IE is extremely high despite the development of preventive and antibiotic therapy. We report a 13-year-old female whose previous medical history includes Jeune syndrome and mitral regurgitation. She was taken to a nearby hospital because of high body temperature. She had no symptoms of cold or gastrointestinal disturbance and was diagnosed with upper respiratory tract inflammation. On the subsequent day, she experienced a seizure and was brought to the emergency department of the general hospital. Her head computed tomography (CT) revealed bleeding and mild cerebral edema in the left occipital lobe. A mild systolic murmur was audible upon auscultation. She presented with carious tooth and Janeway lesions. Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) was positive on blood culture examination, cerebrospinal fluid examination was negative. A diagnosis of IE was established based on the Duke criteria. Antibiotic therapy was administered. Thereafter, the symptoms disappeared without any adverse effects, and antibiotic administration was ended in six weeks. After the discharge, dental treatment was initiated. There was no recurrence of IE at 3 years after the onset, and no sequelae were observed. Although the prevalence of cerebral hemorrhage as a complication of IE is low, the associated mortality rate is extremely high despite the development of preventive and antibiotic therapy. Moreover, there is no consensus regarding the treatment method. In this case, only a conservative treatment was performed without sequelae. Pediatric patients with stroke associated with IE may have better outcome than adults. It is important to suspect IE and to provide immediate or early treatment if fever and central nervous symptoms are observed in cases with underlying heart disease.