The reaction of three types of carbon nanofibers (CNFs; platelet: CNF-P, tubular: CNF-T, herringbone: CNF-H) with [Ru3(CO)12] in toluene heated at reflux provided the corresponding CNF-supported ruthenium nanoparticles, Ru/CNFs (Ru content=1.1–3.8 wt %). TEM studies of these Ru/CNFs revealed that size-controlled Ru nanoparticles (2–4 nm) exist on the CNFs, and that their location was dependent on the surface nanostructures of the CNFs: on the edge of the graphite layers (CNF-P), in the tubes and on the surface (CNF-T), and between the layers and on the edge (CNF-H). Among these Ru/CNFs, Ru/CNF-P showed excellent catalytic activity towards hydrogenation of toluene with high reproducibility; the reaction proceeded without leaching of the Ru species, and the catalyst was reusable. The total turnover number of the five recycling experiments for toluene hydrogenation reached over 180 000 (mol toluene) (mol Ru)−1. Ru/CNF-P was also effective for the hydrogenation of functionalized benzene derivatives and pyridine. Hydrogenolysis of benzylic CO and CN bonds has not yet been observed. Use of poly(ethylene glycol)s (PEGs) as a solvent made possible the biphasic catalytic hydrogenation of toluene. After the reaction, the methylcyclohexane formed was separated by decantation without contamination of the ruthenium species and PEG. The insoluble PEG phase containing all of the Ru/CNF was recoverable and reusable as the catalyst without loss of activity.