Neuronal damage and axonal regeneration inhibition are the main reasons to poor functional recovery after ischemia. Nogo-A signals inhibit axon outgrowth through the PirB receptor after ischemic reperfusion injury in central nervous system. We use TAT-PEP, a novel protein which could pass through the blood brain barrier, to block the function of PirB and identify the long-term neurological and behavioral recovery after bilateral common carotid artery occlusion (BCCAO) in mice. We observed that TAT-PEP promoted neuron survival and inhibited neuronal apoptosis. TAT-PEP increased the expression of Tau, GAP43 and MAP-2 proteins. In addition, the short-term and long-term cognitive functions were also enhanced, indicating that TAT-PEP had a long-term neuroprotective effect, which reduced neurologic injury and neuron loss, promoted neurite outgrowth and enhanced functional recovery after ischemia. These studies reveal the mechanism of PirB on stroke and offer a potential therapeutic method for cerebral ischemia in humans.