Numerical simulations were carried out for various reacting flow fields related to scramjet propulsion system using commercial CFD Software. Three-dimensional Navier stokes equations were solved along with the K-ε turbulence model. Modeling of the turbulence chemistry interaction is done through infinitely fast rate chemical kinetics. The software was validated extensively by comparing different experimental conditions for scramjet combustor to find its error band and range of application. Good agreement between the experimental and computational values were obtained for the scramjet combustor flow field with strut, pylon and cavity injection system with both hydrogen and hydrocarbon fuel. The validated CFD tool was applied in the design exercise of flight-sized kerosene fuel scramjet combustor of a hypersonic airbreathing mission. Significant improvement of combustion efficiency and thrust could be achieved by relocating the fuel injection system through the analysis of various thermochemical variables in the scramjet combustor.