R&D on hydrogen energy technology had been conducted in world energy network (WE-NET) Project in Japan, which was followed by the project “Development of Safe Utilization Technology and an Infrastructure for Hydrogen Use” with the emphasis on the fuel cell deployment. These projects, both supported by New Energy and Industrial Technology Development Organization (NEDO), have contained the subproject “Research on Innovative Technologies” to ensure discovery and incubation of innovative technologies that are considered indispensable for introduction and dissemination of hydrogen energy into the society. In this paper, some significant results achieved in this subproject together with the framework of the project will be reported. In the exploratory research on the alternative materials to platinum group metals for fuel cells and hydrogen production, tantalum oxynitrides were found potentially applicable as new electrodes; the development of magnetic refrigeration of hydrogen is under way with the finding of materials with feasible magneto-caloric properties; in search of innovative hydrogen storage systems, a new process of decalin dehydrogenation/naphthalene hydrogenation based on superheated liquid-film-type catalysis was developed.