The spatio-temporal evolution of the energetic particles in the transport time scale in tokamak plasmas is a key issue of the plasmas confinement, especially in burning plasmas. In order to include sources and sinks and collisional slowing down processes, a new solver, ATEP-3D was implemented to simulate the evolution of the energetic particle (EP) distribution in the three-dimensional constants of motion (CoM) space. The Fokker–Planck collision operator represented in the CoM space is derived and numerically calculated. The collision coefficients are averaged over the unperturbed orbits to capture the fundamental properties of EPs. ATEP-3D is fully embedded in ITER IMAS framework and combined with the LIGKA/HAGIS codes. The finite volume method and the implicit Crank-Nicholson scheme are adopted due to their optimal numerical properties for transport time scale studies. ATEP-3D allows the analysis of the particle and power balance with the source and sink during the transport process to evaluate the EP confinement properties.