Oxidative stress is responsible for the pathogenesis of many diseases, and antioxidants are commonly included in their treatment protocols. Over the past two decades, numerous biomedical reports have revealed the therapeutic benefits of molecular hydrogen (H₂) in relieving oxidation-related diseases. H₂ has been found to have selective antioxidant properties against the most dangerous oxidants (hydroxyl radicals and peroxynitrite). H₂ demonstrates numerous biologically therapeutic properties, including anti-inflammatory, antioxidant, anti-cancer, anti-stress, anti-apoptotic, anti-allergic effects, signaling molecule functions, regulation of redox balance, modulation of antioxidant enzyme gene expression, improvement of blood vessel function, down-regulation of pro-inflammatory cytokines, stimulation of energy metabolism, and protection of the nervous system. Experimental and clinical studies have shown the potential use of hydrogen nutrition therapy for ameliorating various diseases, including cardiovascular, respiratory, and metabolic disorders, as well as obesity, gastrointestinal disorders, and brain and nervous system disorders. The administration methods of hydrogen include inhalation, hydrogen-rich water, hydrogen-rich saline, hydrogen-rich eye drops, and hydrogen-rich bathing. Hydrogen nutritional therapy can be applied to different diseases, and it offers a natural alternative to chemical and radiation therapies. This review covers the different administration methods and the latest experimental and clinical research on the potential applications of H₂ in nutritional therapy for different diseases.