The present invention relates to a pharmaceutical composition for the prevention and treatment of blood-brain barrier disorder comprising fluoxetine as an active ingredient. More particularly, fluoxetine inhibits the expressions of matrix metalloproteinase(MMP)-2, MMP-9, and MMP-12, which are reported to be related to blood-brain barrier (BBB) disruption and inflammatory reaction after spinal cord injury, specifically inhibits the activations of MMP-2 and MMP-9, inhibits the decomposition of ZO-1, the most representative tight junction protein, so as to maintain tight junction between endothelial cells and to protect blood-brain barrier thereby, inhibits the increase of blood-brain barrier permeability, and inhibits the expressions of chemoattractants of blood cells, such as CXCL-1, CXCL-2, CCL-2, CCL-3 and CCL-4 so as to reduce inflow of blood into spinal cord and recover exercise function which has been deteriorated by spinal cord injury. Therefore, fluoxetine can be effectively used for the prevention and treatment of central nervous system disease, blood-brain barrier disorder, or blood-spinal cord barrier disorder.