While Jupiter’s gravity strongly binds the neutral atmosphere to the planet, energization in the auroral region can lead to field-aligned upward transport and escape of electrons and ions. This field-aligned transport mechanism provides a way for heavier ions like H2+ and H3+ to enter Jupiter’s magnetosphere. Formation of H3+ from H2+ occurs quickly in the collisional ionosphere, so rapid field-aligned transport of H2+ is the most likely mechanism for H2+ ions present in Jupiter’s high-latitude ionosphere and magnetosphere. We model these processes using the PWOM model for ionospheric field-aligned transport and J-GITM providing the neutral atmosphere and lower ionospheric boundary. The ionosphere is formed and heated by a combination of solar EUV flux and electorn precipitaiton. The effects of energization from electron precipitation and resonant wave heating are also accounted for. We show the energy input that is needed to produce ion escape in both the fluid and kinetic regimes, and we show the formation of ion conics in the kinetic PWOM model. We discuss what observations from JUNO are needed to allow us to constrain and test our model results.