Jupiter’s moon Ganymede possesses a tenuous atmosphere, as part of which atomic hydrogen has been detected in an extended exosphere by the Galileo spacecraft and the Hubble Space Telescope (HST). Here, we analyse temporally resolved Lyman-α observations from HST’s Space Telescope Imaging Spectrograph (STIS) of Ganymede in eclipse and after egress to investigate the behaviour hydrogen bearing species in the atmosphere. Atomic hydrogen is probed via resonant scattering of solar Lyman-α radiation at 121.6 nm and can therefore be observed immediately after but not during eclipse, when possible auroral Lyman-α emission is instead examined. We use an observation beginning at egress to determine whether the H component underwent depletion or collapse while Ganymede was in Jupiter’s shadow. The H surface number densities inferred from radial Lymanα brightness profiles recorded directly after eclipse match the values derived from subsequent exposures and are similar to previously reported densities. This absence of depletion suggests that Ganymede’s hydrogen exosphere remains largely unaffected by eclipse. These findings support hydrogen production mechanisms that operate independently of sunlight. Finally, unlike the bright electron-impact–driven 1356 Å oxygen aurora, we find no conclusive evidence for localized Lyman-α auroral emission from hydrogen-bearing species in eclipse.