Baikal skullcap (Scutellaria baicalensis Georgi) is one of the most widely used medicinal plants in traditional Eastern medicine, especially in Chinese medicine. Its major phytochemicals are flavonoids (aglycones, glycosides and their glucoronides) such as baicalin, baicalein, wogonin, and wogonoside. S. baicalensis and its flavonoids exert several pharmacological activities, including antiallergic, antioxidant, anti-apoptic, anti-inflammatory effects and many more. Recently, Baikal skullcap and its isolated flavonoids have been studied for their neuroprotective effects in a variety of in vitro and in vivo models of neurodegenerative diseases. Results showed significant neuroprotective effect of these natural substances. In this review, we focus on the neuroprotective effects of Baikal skullcap and its flavonoids on the nervous system, in particular its antidepressant, anticonvulsant and anxiolytic effects and their influence on the cognitive functions of the brain.