This study investigated the effects of baicalein, a natural compound isolated from the root of scutellaria, on cognitive and motor ability impaired by chronic cerebral hypoperfusion in rats, as well as its effects on brain mitochondria. Rats subjected to permanent bilateral common carotid artery occlusion experienced cognitive deficits, oxidative stress and mitochondria dysfunction, which was associated with the elevation of reactive oxygen species level, the decrease of oxidative phosphorylation parameters, the loss of mitochondrial membrane potential, the reduce in Bcl-2/Bax ratio, and the release of cytochrome c. Baicalein alleviated cognitive and motor impairments and decreased mitochondria reactive oxygen species production, in accordance with its improvements on membrane potential level, oxidative phosphorylation process, mitochondrial swelling degree, Bcl-2/Bax ratio and cytochrome c release. These data indicated that baicalein might have therapeutic potential for the treatment of dementia caused by chronic cerebral hypoperfusion, contributed to its protections on brain mitochondrial homeostasis and function.