Engine knock and misfire are barriers to pathways leading to high-efficiency Spark-Ignited (SI) Natural Gas engines. The general tendency to knock is highly dependent on engine operating conditions and the fuel reactivity. The problem is further complicated by low emission limits and the wide range of chemical reactivity in pipeline quality natural gas. Depending on the region and the source of the natural gas, its reactivity, described by its methane number (analogous to the octane number for liquid SI fuels) can span from 65–95. In order to realize diesel-like efficiencies, SI natural gas engines must be designed to operate at high BMEP near knock limits over a wide range of fuel reactivity. This requires a deep understanding regarding the combustion-engine interactions pertaining to flame propagation and end-gas autoignition (EGAI). However, EGAI, if controlled, provides an opportunity to increase SI natural gas engine efficiency by increasing combustion rate and the total burned fuel, mitigating the effects of the slow flame speeds of natural gas fuels which generally reduce BMEP and increase unburned hydrocarbon emissions. For this reason, in order to study EGAI phenomenon, the present work highlights multi-dimensional computational fluid dynamics (CFD) models of the Cooperative Fuel Research (CFR) engine. The CFR engine models are used to investigate fuel-engine interactions that lead to EGAI with natural gas, including effects of fuel reactivity, engine operating parameters, and exhaust gas recirculation (EGR). A Three-Pressure Analysis, performed with GT-Power, was used to estimate initial and boundary conditions for the three-dimensional CFD model. CONVERGE CFD v2.4 was used for the three-dimensional CFD modeling where the level set G-Equation model and SAGE detailed chemical kinetics solver were used. An assessment of the different modeling approaches is also provided to evaluate their limitations, advantages and disadvantages, and for which situations they are most applicable. Model validation was performed with experimental data taken with a CFR engine over varying compression ratio, CA50, EGR fraction, and IMEP and shows good agreement in Peak Cylinder Pressure (PCP), PCP crank angle, and the location of the 10%, 50%, and 90% mass fraction burned (CA10, CA50, and CA90, respectively). The models can predict the onset crank angle and pressure rise rate for light, medium, and heavy EGAI under a variety of fuel reactivities and engine operating conditions.