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The aim of this study was to investigate the effect of a BuOH-soluble fraction from Dracocephalum tanguticum Maxim (DME), which contained 52% of total flavonoid, on the cerebral ischemia injury induced by permanent middle cerebral artery occlusion (pMCAO) in rats. RT-PCR and Western blot analysis showed that DME (30 mg/kg/day for seven days) by intragastric administration modulated the mRNA expression and protein synthesis of two neurotrophic factors: brain-derived neurotrophic factor (BDNF) and neurotrophin 3 (NT-3). DME was effective in stimulating BDNF mRNA expression and protein synthesis in the ipsilateral frontal cortex (IFC) of both the sham-operated and pMCAO rats and this effect was also observed in the hippocampus of the pMCAO rats. DME significantly increased NT-3 mRNA expression and protein synthesis in the IFC and hippocampus of the pMCAO rats, although it had no effect on NT-3 expression in the sham-operated groups. Meanwhile, DME also decreased the malondialdehyde contents in the hippocampus of the sham-operated and pMCAO groups, and significantly attenuated the decrease of endogenous antioxidant (superoxide dismutase, glutathione peroxidase and catalase) activities in both the IFC and hippocampus of the rats after ischemia insult injury. Moreover, DME facilitated the neurobehavioral recovery after the cerebral ischemia. These findings suggested that DME has potential for treatment of ischemia-induced brain damage through stimulation of antioxidant activity and neurotrophic factor synthesis.