The present study was done to investigate the possible effects of thymoquinone on the inhibition of activation of NF-kappaB in experimental autoimmune encephalomyelitis in the rat model of multiple sclerosis. Experimental autoimmune encephalomyelitis was induced in Lewis rats by injecting myelin basic protein emulsified in complete freund's adjuvant. Several parameters including clinical signs, perivascular cuffing and infiltration of mononuclear cells in the brain and spinal cord, glutathione levels in the red blood cells and inhibition of the activation of NF-kappaB were determined to assess the degree of protection. The study showed that treatment of rats with thymoquinone 1 mg/kg/day concomitant to myelin basic protein and after the appearance of clinical signs resulted in preventing and ameliorating experimental autoimmune encephalomyelitis. Thymoquinone was able to counter perivascular cuffing and infiltration of mononuclear cells in the brain and spinal cord, increase the red blood cell glutathione, and inhibit the activation of NF-kappaB in the brain and spinal cord. These results were consistent with the clinical signs and suggest a beneficial effect of thymoquinone against experimental autoimmune encephalomyelitis in the rat model of multiple sclerosis.