We have investigated the chemistry of the Jovian auroral thermosphere/ionosphere by modeling the precipitation of high-energy electrons into the auroral zones using a multistream electron-transport code and three model thermospheres: a standard model based on pressure and temperature data from Galileo, and two additional models that are characterized by enhanced eddy diffusion coefficients. We have predicted the effects of precipitation of monoenergetic electrons with energies between 20 and 100 keV with energy fluxes of about 11 ergs cm-2s-1. We have derived the column densities of H2, H, CH4, and C2H2 above the altitudes of peak energy deposition. For methane column densities similar to those determined from IUE and Hubble Space Telescope H2 spectral data, we find that for our standard model, the most likely electron energies are in the 45--55 keV range. For the enhanced eddy diffusion models the energies are lower. We present ion density profiles, H density profiles, and production profiles for the most important H2 and H emissions. The predicted H column densities are in the range (1-6)¿1018 cm-2 for the standard model and are smaller for the enhanced eddy diffusion models. We find that the temperatures near the altitude of peak energy deposition vary from 160 to 200 K and are significantly lower than those derived from rotational analyses of auroral H2 emissions, which average 400--500 K. This indicates that the auroral thermosphere is considerably warmer than those at lower latitudes that were measured by the Voyager spacecraft or the Galileo probe. ¿ 1999 American Geophysical Union