Transverse sonic injection into supersonic cross flow is a well-established technique to inject fuel into a SCRAMJET combustor. A SCRAMJET combustor with a backward facing step acting as a flame-holder has been used for this study. The jet is placed at various locations downstream of the step, where each location represents a distinct flow region. Three-dimensional simulations have been performed using Menter's SST model in our in-house parallel 3-D RANS unstructured grid CFD solver. In such a SCRAMJET configuration, mixing between air and fuel is augmented by shocks generated by the under-expanded jet injected into the supersonic cross flow, hence the jet location is expected to be critical. The performance and mixing of the combustor has been quantified for each of the distinct configurations. The length of the combustor required for complete mixing has also been estimated for the different cases. It is observed that the mixing and performance are strongly affected by the location of the jet in the combustor flow-field. From the results presented in this paper, the optimal location for the jet is somewhat before the end of the recirculation region behind the backward facing step. © 2019 Elsevier Masson SAS