The long-term effect of magnetically targeted neural stem cells in a rat focal cerebral ischemia model was investigated. In middle cerebral artery occlusion (MCAO) stroke model rats, ferumoxide-labeled human neural stem cells (hNSCs) were injected into the tail vein. MCAO rats were divided into three groups: ischemia only (IO), ischemia with NSC injection (IC), and ischemia with NSC injection and the use of magnet targeting (IM). Four weeks after MCAO and 3 weeks posttransplantation, a greater number of hNSCs were found in ischemic lesion sites in IM rat brain compared with IO and IC animals. In addition, differentiation of hNSCs into neurons or astrocytes and angiogenesis were markedly increased. In IM rats, infarct volume was considerably reduced, and function was significantly improved. The present study indicates that long-term use of magnetic fields may be a useful way to improve the efficacy of targeted migration of stem cells and functional deficits in stem cell-based therapy for ischemic brain injury.