A non-invasive method for treating neurodegenerative diseases. Light energy is applied externally to a patient's head to stimulate different neurological pathways, reduce inflammation and stimulate mitochondria function in the brain. The light is applied near the area of the brain that is malfunctioning or that is associated with the source of the disease to be treated. The treatment can be enhanced by activating the cranial nerves while the light is applied.The wavelength of the applied light range from about 400-760 nm, and in a preferred embodiment is about 640 nm. The applied light energy can be applied with a pulse frequencies that mimic healthy brain function of alpha, beta, delta, and theta waves. The pulse frequencies can be applied series, alternately, or simultaneously. The light can be emitted from the same light emitter or from multiple emitters and is preferably laser light.