Flow behavior and thrust performance of MHD energy bypass scramjet engine was examined numerically. MHD generator was placed at the isolator to enhance the flow compression. Kinetic energy was converted to electrical energy in the MHD generator. Extracted electrical energy was consumed at the MHD accelerator placed at the downstream of the combustor. When MHD energy bypass system was used, the flow was decelerated and compressed in the MHD generator. Effect of velocity and Mach number on wall friction was analyzed and decrease of friction force was pointed out. Also, high pressure in the combustor resulted in increase of pressure contribution to net thrust. Despite of positive effects, decelerating Lorentz force in the MHD generator was comparably large and no significant difference in net thrust performance is observed.