The hydrogen oxidation reaction (HOR) in alkaline electrolyte was conducted on carbon-supported Ru nanoparticles (Ru/C) of which size was controlled in the range from approximately 2 to 7 nm. The HOR activity of Ru/C normalized by the metal surface area showed volcano shaped dependence on the particle size with a maximum activity at approximately 3 nm. The HOR activity of approximately 3 nm Ru/C was higher than commercially available Pt nanoparticles (ca. 2 nm) supported on carbon. The structural analysis of Ru/C using Cs-corrected scanning transmission electron microscopy with atomic resolution revealed the unique structural change of Ru/C different from Pt/C: Ru nanoparticle structure changed from amorphous like structure below 3 nm to metal nanocrystallite with roughened surface at approximately 3 nm and then to that with well-defined facets above 3 nm, although Pt/C kept well-defined facets even at approximately 2 nm. It is proposed that the generation of unique structure observed on approximately 3 nm Ru nanoparticles, that is, long bridged coordinatively unsaturated Ru metal surface atoms on its nanocrystallite, is a key to achieve high HOR activity.