High concentration of zinc has been reported to act as a critical mediator of neuronal death in the ischemic brain. Our previous studies showed that labile zinc accumulates in cerebromicrovessels and contributes to blood-brain barrier (BBB) permeability increase after cerebral ischemia. However, the role of mitochondrial zinc in ischemia-induced BBB permeability alteration is still unclear. In this study, we showed that ischemia/reperfusion induced free zinc accumulation in endothelial cells (ECs), resulting in increased generation of reactive oxygen species (ROS) in both cultured ECs and in microvessels isolated from the brain of ischemic rats. Furthermore, we found that zinc was highly accumulated in mitochondria, leading to mitochondrial ROS generation under the ischemic condition. Moreover, zinc overload in mitochondria resulted in the collapse of the network of mitochondria, which was mediated through Dynamin-related protein-1 (Drp-1) dependent mitochondrial fission pathway. Finally, the zinc overload in mitochondria activated matrix metalloproteinase-2 and led to ischemia-induced BBB permeability increase. This study demonstrated that zinc-ROS pathway in mitochondria contributes to the ischemia-induced BBB disruption via Drp-1 dependent mitochondrial fission pathway.