Voyager 2’s passage through the downstream corotation region of Ganymede found disturbances in the field and particle environment. Large fluctuations in the intensities and energy spectra of ions in the 0.1- to 4.0-MeV interval were also observed with the low energy charged particle experiment. All ion species were evidently affected, up through medium (C, N, O) nuclei. Electrons intensities while disturbed, did not behave similarly to the ions. These effects are probably associated with the wake, produced by the absorption of Jovian magnetospheric corotating plasma by Ganymede. We propose a two-dimensional theoretical model for perturbed field in the wake region and show by direct numerical simulation of exact particle trajectories that such perturbations are capable of modulating the charged particle energies to about the observed amount for the observed magnetic and plasma parameters. Analysis shows that the energization process is dependent on the pitch angles of the energetic ions and the process itself is non-adiabatic (the Larmor radius is approximately the size of the disturbance region).