The growth of hydraulic fracking has resulted in a dramatic cost reduction of Compressed Natural Gas (CNG), a low carbon fuel. CNG cannot be used as singular fuel in conventional Compression Ignition (CI) engines because of its high auto-ignition characteristics. However, CNG-assisted diesel combustion represents a means to shift the energy consumption of CI engines away from liquid fossil fuels. Calculation of the rate of heat release is vital for understanding and optimizing this mode of engine operation. A previously constructed three-zone equilibrium heat release model that is calibrated to engine exhaust emission measurements was augmented in order to allow for the addition of CNG in the engine intake. The model was also adapted to permit reuse of unburned CNG gas with other exhaust species via exhaust gas recirculation. This is because experiments demonstrated a potentially significant increase in methane emissions under high CNG flowrates. Specifically, the CNG mixture is modeled as a single lumped chemical species, and is held apart from the intake air within the model. Representative results are given for a high compression ratio single-cylinder CI engine with variable amounts of CNG addition, and the effects of engine phenomena on heat release modeling are discussed.