A model is described for the transport of magnetospheric oxygen ions with low charge state and energies up to several MeV/nucleon (MeV/u) as they precipitate into Jupiter's polar atmosphere. A revised and updated hybrid Monte Carlo model originally developed by Ozak et al. (2010, https://doi.org/10.1029/2010JA015635) is used to model the Jovian X‐ray aurora. The current model uses a wide range of incident oxygen ion energies (10 keV/u to 5 MeV/u) and the most up‐to‐date collision cross sections. In addition, the effects of the secondary electrons generated from the heavy ion precipitation are included using a two‐stream transport model that computes the secondary electron fluxes and their escape from the atmosphere. The model also determines H2 Lyman‐Werner band emission intensities, including a predicted spectrum and the associated color ratio. Implications of the new model results for interpretation of data from National Aeronautics and Space Administration's Juno mission are discussed. In particular, the model predicts that for a 2 MeV/u oxygen ion energy input of 10 mW/m2: (1) escaping electrons are produced with an energy range from 1 eV to 4 keV, which is a smaller range than previous models by Ozak et al. (2013, https://doi.org/10.1002/2013GL50812) predicted, (2) H2 band emission rates of 75 kR are generated, similar to previous estimates, and (3) a newly calculated Lyman and Werner band color ratio of 10 is expected. The color ratios are put into a context of various methane number density distributions.