The paper presents a numerical analysis of the rolling contact between an elastic ellipsoid and an elastic-plastic flat. Numerical simulations have been performed with the help of a contact solver called Plast-Kid®, with an algorithm based on an integral formulation or semi-analytical method. The application of both the conjugate gradient method and the discrete convolution and fast Fourier transform technique allows keeping the computing time reasonable when performing transient 3D simulations while solving the contact problem and calculating the subsurface stress and strain states. The effects of the ellipticity ratio k—ranging from 1 to 16—and of the normal load—from 4.2 GPa to 8 GPa—are investigated. The reference simulation corresponds to the rolling of a ceramic ball on a steel plate made of an AISI 52100 bearing steel under a load of 5.7 GPa. The results that are presented are, first, the permanent deformation of the surface and, second, the contact pressure distribution, the von Mises stress field, the hydrostatic pressure, and the equivalent plastic strain state within the elastic-plastic body. A comparison with an experimental surface deformation profile is also given to validate the theoretical background and the numerical procedure.