Atriventricular septal aneurysm is a rare finding. Thrombus within the atrioventricular septal aneurysm has never been reported. Here, we report a girl with sudden-onset hemiparesis. Magnetic resonance imaging of the patient’s head revealed a lesion at the right basal ganglion. Cerebral infarction was impressed. A series of examinations was performed to find the source of the cerebral embolism. Transthoracic echocardiography further showed a thrombus in the aneurysm. A subsequent operation revealed a fresh thrombus in the aneurysm. The presence of an anatomic substrate such as this might justify anticoagulation treatment or even surgical intervention before thromboembolism occurs.