We studied the adsorption, surface diffusion, and penetration, i.e. the initial processes of a Ni adatom on the H-terminated Si(001)-(2 x 1) surface by the first-principles theoretical calculations. As concerns the adsorption, Two different types were found. When Ni is deposited onto the Si dimer row, it once captures H from the dimer Si, though it eventually returns H, with no activation energy barrier. Then, Ni moves to the most stable site, which is the off-centered bridge (B) site between the dimer rows, with the activation energy of 0.65 eV. On the other hand, Ni deposited between the dimer rows captures no H and moves to the B site without the energy barrier. Thus an adsorbed Ni atom invariably arrives at the most stable B site at the room temperature. As for the surface diffusion, it needs the activation energies of 0.66 and 1.19 eV for Ni to migrate from the B site in the directions parallel and perpendicular to the dimer row, respectively. Therefore, we concluded that the surface diffusion of Ni is restricted in the valley between the dimer rows at the room temperature. Furthermore, since the penetration of Ni is blocked on this surface, it was also concluded that the surface hydrogenation suppresses silicidation.