The electrodynamic interaction of Ganymede’s mini-magnetosphere with Jupiter’s corotating magnetospheric plasma has been shown to give rise to strong current systems closing through the moon and its ionosphere as well as through its magnetopause and magnetotail current sheet. This interaction is strongly evidenced by the presence of aurorae at Ganymede and of a bright Ganymede footprint on Jupiter’s ionosphere. This footprint is located equatorward of the main auroral emissions, at the magnetic longitude of the field line threading Ganymede. The brightness of Ganymede’s auroral footprint at Jupiter along with its latitudinal position have been shown to depend on the position of Ganymede relative to the center of the Jovian plasma sheet. Additionally, observations using the Hubble Space Telescope showed that Ganymede’s auroral footprint brightness is characterized by variations of three different timescales: 5 hours, 10-40 minutes, and ~100 seconds. The goal of the present study is to examine the relationship between the longest and the shortest timescale periodicities of Ganymede’s auroral footprint brightness and the local processes occurring at Ganymede. This is done by coupling a specifically developed brightness model to a three-dimensional multifluid model which tracks the energies and fluxes of the various sources of charged particles that precipitate into Ganymede’s ionosphere to generate the aurora. It is shown that the predicted auroral brightnesses and morphologies agree well with observations of Ganymede’s aurora from the Hubble Space Telescope. Our results also suggest the presence of short- and long-period variabilities in the auroral emissions at Ganymede due to magnetic reconnections on the magnetopause and in the magnetotail, and support the hypothesis of a correlation between the variability of Ganymede’s auroral footprint on Jupiter’s ionosphere and the variability in the brightness and morphology of the aurora at Ganymede. Finally, the modeled aurora at Ganymede reveals that the periodicities in the morphology and brightness of the auroral emissions are produced by two different dynamic reconnection mechanisms. The Jovian flow facing side aurora is generated by electrons sourced in the Jovian plasma and penetrating into Ganymede’s ionosphere through the cusps above the separatrix region. In this case, the reconnection processes responsible for the auroral emissions occur on Ganymede’s magnetopause between the Jovian magnetic field lines and the open magnetic field lines threading Ganymede’s Polar Regions. As for the magnetotail side aurora, it is generated by electrons originating from Ganymede’s magnetospheric flow. These electrons are accelerated along closed magnetic field lines created by magnetic reconnection in Ganymede’s magnetotail, and precipitate into Ganymede’s ionosphere at much lower latitudes, below the separatrix region.