Infective endocarditis (IE) is caused by infection of the endocardial surface of heart. It typically affects one or more heart valves, the mural endocardium, or a septal defect. In recent years, many IE patients suffered from atypical initial symptoms. Here, in this case report, a 12-year-old patient was initially diagnosed as encephalitis. However, it was later noticed that this was a misdiagnosis for the following reasons: the echocardiography showed a vegetation attached to his mitral valves; the cranial magnetic resonance imaging showed lesions that were consistent with a cardioembolic distribution. The final diagnosis was IE.