Highly Oriented Pyrolitic Graphite presents a layered structure. In this work, we propose a theoretical and computational model for taking into account the anisotropic structure of graphite in the Monte Carlo simulations of charge transport. In particular, the dielectric characteristics, such as the inelastic mean free path and energy losses, are treated by linearly combining the contribution to these observables along the two main orthogonal directions identifying the crystalline structure (along the layer plane and perpendicular to it). Energy losses are evaluated from ab initio calculations of the dielectric function of the system along these two perpendicular directions. Monte Carlo simulated spectra, obtained with this approach, are compared with acquired experimental data of Reflection Electron Energy Loss and Secondary Electron spectra showing a good agreement. These findings validate the idea of the importance of considering properly-weighted inter-planar and intra-planar interactions in the simulation of electron transport in layered materials.