It is believed that most of the experimental data on hypersonic boundary layer transition obtained from conventional ground testing facilities are not reliable due to high levels of noise associated with the acoustic fluctuations from the turbulent boundary layers on the wind tunnel walls. Therefore, it is very important to have quiet testing facilities for hypersonic flow research. The Boeing/AFOSR Mach 6 Wind Tunnel at Purdue University has been designed as a quiet tunnel for which the noise level is an order of magnitude lower than that in conventional wind tunnels. However, quiet flow was achieved in the tunnel only for low Reynolds numbers. Early transition of the nozzle wall boundary layer was identified as the cause of the test section noise. On the basis of detailed experimental measurements, the most likely causes for the early transition are identified to be separation bubbles near the bleed lip and fluctuations generated at the nozzle throat due to the bleed slot. In this study, the existence of steady and unsteady separation bubbles on the main flow and the bleed flow side of the nozzle lip of the tunnel are investigated numerically and a new geometry is designed by changing the nozzle lip of the tunnel to eliminate the separation bubbles on both sides of the bleed lip.