The present study evaluated the potential neuroprotective effect and underlying mechanism of the total flavones extracted from Chrysanthemum morifolium (TFCM) against ischemia/reperfusion (I/R) injury. An animal model of cerebral ischemia was established by occluding the right middle cerebral artery for 90 minutes followed by reperfusion for 22 hours. The neurobehavioral scores, infarct area, and hemispheric edema were evaluated. The superoxide dismutase (SOD) activity, malondialdehyde (MDA) content, and reactive oxygen species (ROS) level in brain were also measured. The results showed that pretreatment with TFCM significantly decreased the neurological deficit scores, percentage of infarction, and brain edema and attenuated the decrease in SOD activity, the elevation of MDA content, and the generation of ROS. In isolated brain mitochondria, $Ca^{2+}$-induced swelling was attenuated by pretreatment with TFCM, and this effect was antagonized by atractyloside. These results showed that pretreatment with TFCM provides significant protection against cerebral I/R injury in rats by, at least in part, its antioxidant action and consequent inhibition of mitochondrial swelling.