Fast and accurate prediction of the nonlinear evolution of instability waves in high-speed boundary layers requires specialized numerical algorithms, and augmenting limited observation in this extreme flow regime is challenging. The deep operator networks (DeepONet) has been shown to be an effective tool for providing accurate and fast physics-informed predictions. DeepONet is trained to map an incoming perturbation to the associated downstream flow field within the nonlinear flow regime. The training is performed using high-fidelity data from direct numerical simulations of the compressible Navier–Stokes equations, when the gas can be approximated as calorically perfect and when chemical non-equilibrium effects must be computed. The performance and requirements of training the DeepONet in each case are evaluated. In addition, we show that informing the training of the DeepONet with the continuity equation improves the accuracy of the results, especially in absence of sufficient training data. Success of the physics-informed DeepONet to predict missing fields depends on the observables. Specifically, prediction of a unique solution depends on the available measurements. These results are a promising step towards applications of neural operator networks to more complex high-speed flow configurations and to data assimilation.