Nanometer-sized materials attract much attention because their physical and chemical properties are substantially different from those of bulk materials owing to their size and surface effects. In this work, neutron powder diffraction experiments on the nanoparticles of palladium hydride, which is the most popular metal hydride, have been performed at 300, 150, and 44 K to investigate the positions of the hydrogen atoms in the face-centered cubic (fcc) lattice of palladium. We used high-quality PdD0.363 nanocrystals with a diameter of 8.0 ± 0.9 nm. The Rietveld analysis revealed that 30% of D atoms are located at the tetrahedral (T) sites and 70% at the octahedral (O) sites. In contrast, only the O sites are occupied in bulk palladium hydride and in most fcc metal hydrides. The temperature dependence of the T-site occupancy suggested that the T-sites are occupied only in a limited part, probably in the subsurface region, of the nanoparticles. This is the first study to determine the hydrogen sites in metal nanoparticles.