Three-dimensional simulations of a practical scramjet inlet is performed to study the shock-boundary layer interaction in the inlet duct. The cowl shock interacts with the boundary layers on the side wall and the opposite wall. Numerical simulations provide a detailed understanding of the complex threedimensional flow separation and shock structure. Further, effect of the location and strength of expansion fans upstream of the shock impingement point is investigated. It is found that a careful placement of the expansion corners can limit the extent of the separation region significantly