To date, there is limited knowledge on the topic of unsteady nonlinear transonic flow caused by large-amplitude excitations. The Certification Specifications for Large Aeroplanes, however, demand loads computations for large-amplitude excitations, e.g., for gust encounters of an aircraft. In this paper, numerical solutions to the unsteady Reynolds-averaged Navier–Stokes equations will be used to analyze gust responses of a transport aircraft configuration for a variety of sinusoidal gusts with different lengths and amplitudes at different Mach numbers. On the one hand, it is shown that unsteady nonlinear responses can lead to lower maximum lift values compared to their time-linearized reference due to unsteady shock-induced flow separation. This nonlinear effect dominates for large gust lengths and higher Mach numbers. On the other hand, for the lowest Mach number considered, the coalescence of a double shock at medium gust lengths introduces nonlinear effects leading to an overprediction of the time-linearized maximum lift by the nonlinear computations. Though the turbulence model of Spalart and Allmaras shows completely different separation patterns than a differential Reynolds stress model, the variation of the turbulence model does not alter the overall qualitative findings, but has an effect on the quantitative values.