Cerebral ischemia-reperfusion injury (CIRI) represents a critical barrier to effective stroke treatment, characterized by mitochondrial dysfunction and neuroinflammatory cascades. Although idebenone (IDE), a CoQ10 analog with potent antioxidant properties, has shown therapeutic potential, its poor mitochondrial accumulation and pharmacokinetic limitations have hindered clinical efficacy. To overcome these challenges, we synthesized W1a, a novel IDE derivative conjugated to the mitochondria-targeting peptide SS-20, designed to enhance mitochondrial localization and pharmacodynamic activity. We demonstrated that W1a significantly ameliorated glutamate-induced oxidative injury in HT22 hippocampal neurons by preserving mitochondrial membrane potential (MMP), enhancing adenosine triphosphate (ATP) production, reducing reactive oxygen species (ROS) accumulation, and maintaining mitochondrial morphology. In vivo, W1a conferred robust neuroprotection in a murine model of transient middle cerebral artery occlusion (tMCAO), as evidenced by reduced infarct volume, improved survival rates, and enhanced neurological recovery. Mechanistically, transcriptomic and biochemical analyses revealed that W1a restored mitochondrial gene expression, elevated NAD+/NADH and ATP levels, suppressed ROS overproduction, and downregulated pro-inflammatory signaling pathways. Moreover, W1a inhibited microglial and astrocytic activation, further supporting its anti-inflammatory efficacy. Collectively, our findings establish W1a as a potent neuroprotective agent that targets mitochondrial dysfunction and neuroinflammation drivers of CIRI pathology, offering a promising therapeutic strategy for ischemic stroke.