In this study, the effects of Polygala tenuifolia root extract on brain ischemia/reperfusion injury in Mongolian gerbils were investigated. The gerbils were administered ethanol extract of P. tenuifolia and its four sub-fractions orally 2 hours prior to ischemia, and were subjected to a 20-minute no-flow cerebral ischemia in vivo. Thirty minutes and 72 hours after reperfusion, the brain was removed and the ATP, lactate and lipid peroxide levels were determined, and the neurons in the hippocampal CA1 subfield were examined. In the vehicle-treated ischemic gerbils, the brain ATP levels decreased significantly, but this decrease was prevented by pre-treatment with an n-butanol fraction of P. tenuifolia. In contrast, both the lactate content and lipid peroxidation levels were elevated in the vehicle-treated ischemic animals, but this elevation was inhibited by ethanol extract and n-butanol fraction of P. tenuifolia, respectively. Both the ethanol extract and n-butanol fraction of P. tenuifolia attenuated post-ischemic neuronal necrosis in the hippocampal CA1 subfield. Our findings suggest that both ethanol extract and n-butanol fraction of P. tenuifolia root can reduce brain damage during ischemia and reperfusion, and prevent lipid peroxidation and preserve the energy metabolism.