Cerebral ischemia/reperfusion (I/R) injury severely threatens human life, while the potential mechanism underlying it is still need further exploration. The rat model of cerebral I/R injury was established using middle cerebral artery occlusion (MCAO). The rat microvascular endothelial cell line bEND.3 was exposed to oxygen-glucose deprivation/reperfusion (OGD/R) to mimic ischemic condition in vitro. Evans blue was performed to determine the blood-brain barrier (BBB) permeability. Real-time PCR and western blot were performed to determine gene expression in mRNA and protein level, individually. Luciferase reporter assay was conducted to determine the relationship between miR-539 and MMP-9. The infarct volume and BBB permeability of cerebral (I/R) rats were significantly greater than Sham group. The expression of miR-539 was decreased, while MMP-9 was increased in the brain tissues of I/R injury rats and OGD/R pretreated bEND.3. Up-regulated miR-539 in OGD/R pretreated bEND.3 significantly promoted the BBB permeability. MiR-539 targets MMP-9 to regulate its expression. OGD/R treatment significantly promoted the BBB permeability in bEND.3, miR-539 mimic transfection abolished the effects of OGD/R, while co-transfected with pcDNA-MMP-9 abolished the effects of miR-539 mimic. MiR-539 targets MMP-9 and further regulates the BBB permeability in cerebral I/R injury.