Phonons are the main contributors to thermal energy transfer in thin films. The size dependence of the thermal transport characteristics alters the film properties such as thermal conductivity. Hence, in the present study, three-dimensional, transient phonon transport in dielectric material is studied through the Equation of Phonon Radiative Transport (EPRT) to assess the size dependence of thermal conductivity. The numerical scheme is introduced solving the EPRT in three dimensions and the governing algorithm is described in detail. A parametric study is carried out examining the effect of the \mathrm{Kn} number on the thermal energy transport characteristics in three-dimensional thermally excited film. The formulation and estimation of the effective thermal conductivity tensor is presented and discussed, thereby extending, to some extent, the one-dimensional results obtained earlier. We demonstrate that thermal conductivity changes in all directions, depending on the size effect. In addition, the directions of the temperature gradient and heat flux vectors differ as the \mathrm{Kn} number approaches unity.