One of the beneficial effects of molecular hydrogen (H 2 , hydrogen gas) is neuroprotection and prevention of neurological disorders. It is important and useful if taking H 2 every day can prevent or ameliorate the progression of neurodegenerative disorders, such as Parkinson’s disease or Alzheimer’s disease, both lacking specific therapeutic drugs. There are several mechanisms of how H 2 protects neuronal damage. Anti-oxidative, anti-inflammatory, and the regulation of the endocrine system via stomach-brain connection seem to play an important role. At the cellular and tissue level, H 2 appears to prevent the production of reactive oxygen species (ROS), and not only hydroxy radical (•OH) but also superoxide. In Parkinson’s disease model mice, chronic intake of H 2 causes the release of ghrelin from the stomach. In Alzheimer’s disease model mice, sex-different neuroprotection is observed by chronic intake of H 2 . In female mice, declines of estrogen and estrogen receptor-β (ERβ) are prevented by H 2 , upregulating brain-derived neurotrophic factor (BDNF) and its receptor, tyrosine kinase receptor B (TrkB). The question of how drinking H 2 upregulates the release of ghrelin or attenuates the decline of estrogen remains to be investigated and the mechanism of how H 2 modulates endocrine systems and the fundamental question of what or where is the target of H 2 needs to be elucidated for a better understanding of the effects of H 2 .