Many attempts have been made to model X‐ray emission from both bremsstrahlung and ion precipitation into Jupiter's polar caps. Electron bremsstrahlung modeling has fallen short of producing the total overall power output observed by Earth‐orbit‐based X‐ray observatories. Heavy ion precipitation was able to reproduce strong X‐ray fluxes, but the proposed incident ion energies were very high ( urn:x-wiley:jgra:media:jgra55396:jgra55396-math-00011 MeV per nucleon). Now with the Juno spacecraft at Jupiter, there have been many measurements of heavy ion populations above the polar cap with energies up to 300–400 keV per nucleon (keV/u), well below the ion energies required by earlier models. Recent work has provided a new outlook on how ion‐neutral collisions in the Jovian atmosphere are occurring, providing us with an entirely new set of impact cross sections. The model presented here simulates oxygen and sulfur precipitation, taking into account the new cross sections, every collision process, the measured ion fluxes above Jupiter's polar aurora, and synthetic X‐ray spectra. We predict X‐ray fluxes, efficiencies, and spectra for various initial ion energies considering opacity effects from two different atmospheres. We demonstrate that an in situ measured heavy ion flux above Jupiter's polar cap is capable of producing over 1 GW of X‐ray emission when some assumptions are made. Comparison of our approximated synthetic X‐ray spectrum produced from in situ particle data with a simultaneous X‐ray spectrum observed by XMM‐Newton shows good agreement for the oxygen part of the spectrum but not for the sulfur part