Ischemia-reperfusion injury impairs the efficacy of reperfusion therapy after ischemic stroke. cyclophilin D (cypD)-mediated openings of mitochondrial permeability transition pore (mptp) and subsequent monocyte-mediated inflammation are considered as major mechanisms of reperfusion injury. However, no medical therapies are currently available. Therefore, we have tested a hypothesis that simultaneous targeting of mPTP and inflammation confers substantial neuroprotection after cerebral ischemia-reperfusion. To address this point, we prepared CypD knockout mice, CC chemokine receptor 2 (CCR2) knockout mice and CypD/CCR2 double knockout mice. These mice were subjected to 60 min transient cerebral ischemia by occluding middle cerebral arteries. Neurological deficits evaluated 3 days after reperfusion were significantly attenuated in CypD/CCR2 double knockout mice as compared to wild-type mice and other single knockout mice. Then, we have prepared polymeric nanoparticles containing cyclosporine A (CsA-NPs) and pitavastatin (Pitava-NPs), targeting mPTP opening and inflammation, respectively. Simultaneous administration of CsA-NP and Pitava-NP at the time of reperfusion also decreased infarct size and attenuated neurological deficits as compared to control nanoparticles and single administration of CsA-NPs or Pitava-NPs. These results indicate that simultaneous targeting of the mPTP opening and monocyte-mediated inflammation could be a novel strategy for better neurological outcomes in patients with ischemic stroke. Innovative therapeutic strategies for protecting the brain from ischemia-reperfusion (IR) injury are necessary to decrease infarct volume and improve clinical outcomes after reperfusion therapy for the treatment of ischemic stroke 1 .Within several minutes after reperfusion, opening of mitochondrial permeability transition pore (mPTP) triggers cell deaths in tissues exposed to IR injury 2. Inflammatory monocytes, Ly6C high CCR2 + in mice or CD14 high CD16 − in humans, accumulate to the cerebral tissue as early as several hours after reperfusion and also trigger cell death 3-8. Cyclosporine A (CsA) is a widely used drug after organ transplantation which binds to cyclophilin A and inhibits calcineurin activities in T cells, and thus exerts immunosuppressive effects. CsA also binds to cyclophilin D (CypD), which results in inhibition of mPTP opening and subsequent cell deaths 9. In experimental animals, intravenous administered CsA decreases infarct size 10. In clinical trials, however, intravenously administered CsA (2.0 mg/kg) failed to improve neurological outcomes after ischemic stroke 11 .This discrepancy raises at least two possibilities. First, monotherapy targeting only mPTP was insufficient in humans. Second, drug delivery to target organ was insufficient. In this study, we prepared mice lacking both CypD and CCR2 to elucidate whether targeting two mechanisms, i.e. mPTP opening and inflammation, confers substantial neuroprotection as evidenced by