In this paper, a hypersonic inlet for operating at Mach 5.0 is designed and analyzed numerically. The main axis of this study is a series of three-dimensional simulations with the accuracy of 10E-06 which are applied to determine the effects of the highly developed boundary layer on the performance of inlet for three different study cases. The basic inlet concept is designed by integration of double ramp compression surface and inlet duct which can reduce the free-stream Mach number to the range of 2.0. The most important factor that it affects the performance of the hypersonic inlet system, is the developed entropy layer on the fuselage of the flight vehicle. Ingestion of this layer results in thermal gradients and pressure recovery losses. The bow shocks at the nose and the leading edges are the main sources of this low kinetic energy layer. Using the k-ω turbulence model in the numerical simulations have resulted in a reliable estimation of the boundary layer. In the current context, shock structures, shock-boundary layer interactions, flow quality at the end of the diffuser and also the effects of using sidewalls on the performance of the hypersonic inlet are the main goals of the simulations and the related results are summarized