This study presents the numerical investigation of a non-axisymmetric hypersonic vehicle, modeled after the X-51 concept, flying at an altitude of 90 km. Due to the low atmospheric density at this altitude and the transitional flow regime, the Direct Simulation Monte Carlo (DSMC) method is employed to accurately capture rarefied effects and molecular collisions. The vehicle’s geometry, specifically its inlet design, is examined for its ability to ensure sufficient mass flow and pressure required for scramjet operation under at that altitude. Key outputs include the shock structures and positions and local flow field properties, which elucidate the influence of non-axisymmetric design on the inlet’s performance. Results indicate that inlet efficiency, characterized by uniform flow distribution and total pressure increase.