Atherosclerotic lesions at the aortic arch are recognized as critical sources of embolic strokes. However, there have been few case reports of aortic arch thrombus occurring without atherosclerotic changes, especially those related to iron deficiency anemia (IDA). A 44-year-old woman was admitted due to rapid-onset right hemiparesis and aphasia. Etiological investigations for cerebral infarction revealed no abnormality other than IDA. This is a rare case of cerebral embolic infarction caused by an aortic arch thrombus with IDA in a middle-aged woman.