The aim of this study is to evaluate the neurotoxicity of methotrexate (MTX) in mice, as well as the neuroprotective effects of wheat germ oil (WGO). One group of mice received corn oil orally for 10 days and a single dose of methotrexate (20 mg/kg) intraperitoneally on the 7th day. Another group was given both wheat germ oil orally for 10 days and methotrexate single dose (20 mg/kg) intraperitoneally on the 7th day. Our results suggest that the administration of MTX produced neurochemical and neurotoxic alterations in the brain causing severe damage including peripheral neuropathy and encephalopathy. It also led to brain tissue-damage by reactive oxygen species (ROS) generation, caused alteration in mitochondrial permeability and tissue injury as a response to the oxidative stress. WGO has neuroprotective action through scavenging the oxygen free radicals, decreasing lipid peroxidation and ameliorating the histopathological changes induced by MTX. WGO is recommended to patients undergoing MTX treatment.