Reynolds-Averaged Navier–Stokes (RANS) simulations, both steady and unsteady, are used to investigate supersonic, chemically reacting, flow fields inside a strut-stabilised supersonic combustion ramjet (scramjet) engine operating under different fuel flow rates. Fully supersonic, fully subsonic and mixed modes of operations inside the combustor, obtained at different fuel flow rates, are studied numerically through shock wave visualisations and top-wall static-pressure probing. The effect of changing fuel flow rates, imposed both suddenly and gradually, on the behaviour of shock waves and wall pressure profiles are studied in detail. For certain modes of combustion characterised by the presence of oblique shocks at the strut, shockwaves in the combustor respond predictably to an increase or decrease in fuel flow rate attaining the steady state flow fields as predicted by RANS simulations for those fuel flow rates. For certain other modes of combustion, characterised by the presence of shockwaves in the isolator and the absence of oblique shocks at the leading edge of the strut, shockwaves in the flow field appear unstable to fuel flow rate modulations. For such cases, any change in fuel flow rates, sudden or gradual, increase or decrease, causes the isolator shocks to immediately move upstream and eventually out of the isolator. A plausible physics-based explanation of the observed phenomena is presented.