An ideal scramjet intake is designed to efficiently capture, compress and heat the hypersonic airflow, preparing it for combustion in the combustion chamber. Intake’s start-unstart behavior is a significant design and operational challenge. High fidelity Computational Fluid Dynamics (CFD) tools, with due validation, are increasingly adopted to tackle the design challenge of designing intakes with wider starting margins. Unstarted flow in an intake is a particularly hard problem due to large-scale unsteadiness, overboard-spillage and oscillatory flow behavior. In this study large amplitude oscillatory unstart was studied both experimentally and numerically. A 2D scramjet intake was designed and tested at Hypersonic Shock Tunnel (HST-2) at Indian Institute of Science (IISc) in Ludwieg mode. The intake was designed for \(M_\infty = 6.5\) and Overall Pressure Ratio (OPR) of 40.2. Unstart in the intake was simulated using a flap placed at the exit of the isolator. This served to increase the imposed back-pressure thus initiating unstart. Numerical computations were also carried out on the geometry. Simultaneous pressure and Schlieren visualisation obtained from experiments were compared against numerical results. The numerical results were in reasonable agreement with the experimental results for the started scenarios, at low Throttle Ratio (TR). The unsteady simulations performed for an intake operating at high TR, had substantially larger deviations from the experimental data. In experiments, the intake was found to unstart at \(TR = 0.32\) and the unstart frequency was found to be 433 Hz. However, the intake was not found to unstart until \(TR = 0.35\) in the simulations and oscillated at 100 Hz. This highlights the complexity of the flow phenomena and challenges in simulating hypersonic internal flows with unstart.