This study investigates how Callisto's perturbed electromagnetic environment—generated by the moon's interaction with the low‐energy Jovian magnetospheric plasma—affects the dynamics of high‐energy ions and electrons. We constrain how these perturbed fields influence the energetic particle fluxes deposited onto the top of Callisto's atmosphere between energies of 4.5 keV ≤ E ≤ 11.8 MeV. We use a hybrid simulation to model the variability in Callisto's perturbed electromagnetic environment over a synodic period by considering three representative scenarios of the moon's plasma interaction, corresponding to various distances of the moon to the Jovian magnetospheric current sheet. The local field perturbations are maximized near the center of the sheet (forming, e.g., signatures of field‐line pileup, draping, and Alfvén wings) whereas far from the sheet, a mere superposition of the moon's induced dipole with the background field largely explains the perturbations. We then apply a test‐particle approach to investigate the dynamics of energetic electrons and ions (protons, oxygen, and sulfur) while exposed to these fields. Since electron gyroradii are smaller than Callisto, the field perturbations generate small‐scale non‐uniformities in their flux patterns onto the moon, while the ion flux patterns are more homogeneous. Energetic electrons dominate the number flux onto the atmosphere, whereas ions dominate the energy flux. Over a synodic period, the flux patterns onto Callisto's exobase closely resemble those when the moon is near the current sheet center, since the differential energetic particle fluxes in the ambient plasma decrease by an order of magnitude when the moon travels far outside of the sheet.