An extension of the CRAC model - CRAC:HEPII (Cosmic Ray Atmospheric Cascade: High Energy Proton Induced Ionization) is presented. The model allows one to compute the ion production by high energy protons entering the Earth’s atmosphere. The model is an extension of the CRAC:CRII model and it is focused on the upper part of the stratosphere and mesosphere. The model is also applicable in the low termosphere. The model is based on pre-computed with high statistics ionization yield functions. Therefore, the CRAC:HEPII model is based on a full Monte Carlo simulation of primary proton propagation and interaction with the atmosphere and explicitly considers various physical processes involved in ion production. All simulations were performed using the GEANT 4 simulation tool PLANETOCOSMICS with NRLMSISE 00 atmospheric model. The ionization yield function allows one to compute ion production due to various populations of primary protons in a wide energy range 100 keV –- 20 GeV/nucleon for a given altitude, from about 6.5×10$^{−9}$ g/cm$^2$ (about 200 km a.s.l.) to the sea level considering a given primary proton spectrum. The spacial and height resolution of the model is improved compared to CRAC model. An application of the model for computation of ion production during ground level enhancement events is demonstrated. A quasi-analytical approach, which allows one to compute the ionization yields for events with arbitrary incidence is also presented.