Neurological disorders are the leading cause of disability and the world's second leading cause of death. Despite the availability of significant knowledge to reduce the burden of some neurological disorders, various studies are exploring more effective treatment options. While the human body can repair and regenerate damaged tissue through stem cell recruitment, nerve regeneration in case of injury is minimal due to the restriction on the location of nerve stem cells. Recently, different types of stem cells extracted from various tissues have been used in combination with natural stimuli to treat neurologic disorders in neuronal tissue engineering. Flavonoids are polyphenolic compounds that can induce the differentiation of stem cells into neurons and stimulate stem cell proliferation, migration, and survival. They can also increase the secretion of nutritional factors from stem cells. In addition to the effects that flavonoids can have on stem cells, they can also have beneficial therapeutic effects on the nervous system alone. Therefore, the simultaneous use of these compounds and stem cells can multiply the therapeutic effect. In this review, we first introduce flavonoid compounds and provide background information on stem cells. We then compile available reports on the effects of flavonoids on stem cells for the treatment of neurological disorders.