The paper aims to numerically study the effect of isolator design on shock-augmented mixing in a generic supersonic Ramjet (SCRAMJET) engine and reduce what would be a very complicated thermodynamics+aerodynamic optimization in the design to a simpler aerodynamic one. Changing the length of the isolator section effectively varies the thickness of the boundary layer that is formed in the isolator, which then enters into the SCRAMJET combustor. The study is conducted on a three-dimensional geometry using the Menter's SST model for turbulence on an in-house unstructured grid RANS solver. In this paper, the authors quantify the effect of the incoming boundary layer thickness on the shock-augment air-fuel mixing in the SCRAMJET combustor. It is observed that for the maximum variation in the isolator length, the normalized mixing volume only improves by 7%, which is only a marginally better mixing of air and fuel obtained as with an increase in the isolator length. The authors conclude that the Prandtl-Meyer expansion fan (PMEF) formed at the flame-holder effectively isolates the combustor from the isolator section to a degree that the isolator dimensions can therefore be chosen entirely on considerations of flow homogenization of inlet air before it enters the combustor section of the SCRAMJET engine. Although, the paper analyses a generic SCRAMJET with specific dimensions, the results are more generally applicable than for the specific design actually considered in the paper. Thus this study is also relevant to SCRAMJET engines that may differ radically from our considered design in form and dimensions. © 2022 Elsevier Masson SAS