Objective To investigate the effect of induced pluripotent stem cells (iPSCs) transplantation after the down-regulation of hypoxia-inducible factor (HIF)-2α gene on the treatment of cerebral ischemia injury in rats. Methods Twenty-four male Sprague-Dawley (SD) rats were randomly and evenly divided into the iPSCs treatment, iPSCs+siHIF-2α and phosphate buffer saline (PBS) control groups. The rat models with cerebral ischemia were established by the middle cerebral artery embolization, and reperfusion was carried out 90 min after embolization. At 3 d after reperfusion, iPSCs transplantation, iPSCs+siHIF-2α transplantation or PBS injection were performed. Before and at 2 and 4 weeks after transplantation, neurobehavioral evaluation was performed and the uptake of 18F-fluoro-deoxyglucose (18F-FDG) was measured by micro-positron emission tomography (micro-PET). At 4 weeks after transplantation, the rats were sacrificed and nerve cell markers were detected by immunofluorescence. Results At 2 and 4 weeks after stem cell transplantation, the neurological function scores of the iPSCs treatment group were significantly lower than those in the PBS control group (both P < 0.05), whereas the neurological function scores in the iPSCs+siHIF-2α group were considerably higher than those in the iPSCs treatment group (both P < 0.05). At 2 and 4 weeks after stem cell transplantation, the glucose metabolism levels (injured side/normal side) in the brain of cerebral ischemia rats in the iPSCs treatment and iPSCs+siHIF-2αgroups were significantly increased compared with those in the PBS control group (both P < 0.001). At the 2nd week after stem cell transplantation, the glucose metabolism level in the iPSCs treatment group was significantly higher than that in the iPSCs+siHIF-2α group (P < 0.001). Subsequently, the glucose metabolism level in the iPSCs+siHIF-2α group continued to rise until the 4th week after stem cell transplantation, which was almost identical to but still lower than that in the iPSCs treatment group (P=0.025). Immunofluorescent staining prompted that the transplanted stem cells survived and migrated to the periphery of the infarction area, and a majority of the transplanted stem cells expressed nerve cell markers. Conclusions iPSCs transplantation can be employed to effectively treat cerebral ischemia injury in rats. Down-regulation of HIF-2α gene exerts certain effect upon the therapeutic effect of iPSCs transplantation.