Ischemic stroke is a leading cause of death and disability, and the treatment options are limited. Recent studies demonstrated that the promising applications of gold nanoparticles (Au-NPs) as intrinsic therapeutics; however, little is known about the effect of Au-NPs on cerebral ischemia-reperfusion (I/R) injury. In this paper, the role of Au-NPs on cerebral I/R injury in the rat middle cerebral artery occlusion (MCAO) model was investigated using citrate-capped 5 nm and 20 nm Au-NPs. It was found that 20 nm Au-NPs administration led to remarkable amelioration of neurologic deficits and infarction volumes. Further research revealed that 20 nm Au-NPs elevated the production of anti-inflammatory cytokines, as well as inhibited I/R induced activation of astrocytes and microglias. Moreover, the expressions of anti-apoptotic proteins were up-regulated and the pro-apoptotic molecules were down-regulated in the post-ischemic brains. These effects were opposite in 5 nm group. The above results showed that the neuroprotection of 20 nm Au-NPs was attributable to its anti-inflammatory and anti-apoptotic effect. This study could provide a novel strategy for the treatment of cerebral I/R injury.