Ischemic stroke (IS) is a leading cause of death in the world, and there is still a lack of effective treatments. Ginkgolide B (GB) can antagonize the platelet activating factor receptor and has shown a significant curative effect on cerebral ischemia. However, GB and other drugs for IS have shown poor clinical efficacy due to their inability to cross the blood-brain barrier (BBB). Herein, red fluorescent carbonized polymer dots (CPDs) were developed as biocompatible nanocarriers to deliver GB to the brain tissue. Both in vivo and in vitro experiments verified the ability of GB-CPDs to penetrate the BBB, and GB-CPDs remained in the brain significantly longer than unmodified CPDs. In a rat model of middle cerebral artery occlusion (MCAO), circulatory administration of GB-CPDs effectively reduced cerebral infarct size and neuronal apoptosis, with a significantly better therapeutic effect compared to GB. This study provided a novel GB-based nanodrug that could target the brain with improved efficacy, showing great application potential in central nervous system diseases.