The effect of combined treatment of Bone Marrow Stromal Cells (BMSC) along with long-term quercetin pre-treatment was studied. SCI was induced in rats by compression. Animals were randomly divided into five groups including sham group, groups representing individual treatments and group representing combined treatment. The effects of various treatment groups were estimated using the Blood Spinal Cord Barrier (BSCB) permeability test, estimation of TJ-associated proteins and NF-?B, and motor function test. The spinal cord water content and BSCB permeability were significantly reduced by treatment with BMSC as well as quercetin. Their combined treatment showed a synergistic effect. Moreover, the animals also showed marked improvement in the hind-limb motor-function after the combination treatment. TJ-associated proteins showed a significant increase in expression upon combination treatment. This increase was greater than the individual treatments, indicating a synergistic effect. A significant decrease of NF-?B expression and a significant attenuation of its activity was found to be due to the combination treatment. The combination treatment of BMSC and quercetin caused a reduction in the permeability of BSCB by the up-regulation of proteins associated with TJ. The decreased BSCB permeability causes overall improvement in the SCI symptoms including edema and motor function. It was also concluded that the alleviation of SCI symptoms is mediated by the NF-?B pathway.