We have theoretically studied the initial processes of a Ni adatom on the Si(001) surface based on the first-principles calculation. On this surface, the most stable adsorption site for Ni is the pedestal site on the Si dimer row (DR). From this site, it needs the activation energies of 0.32 and 0.86 eV for the surface diffusion in the directions parallel and perpendicular to the dimer row, respectively. While under the surface, there exist more stable sites, and the minimum value of the activation energies needed for the penetration into these sites from the pedestal site is 0.71 eV. Thus, we have concluded that a Ni atom can readily diffuse on the Si surface and also penetrate into the subsurface, then it finally becomes stable in the subsurface site, at the room temperature (RT). Furthermore, it has also been concluded that the penetration of Ni is the precursor state for silicidation.