This study investigates the capability of wall-modeled large-eddy simulation (WMLES) in predicting the transonic buffet phenomenon over three-dimensional aircraft configurations at high Reynolds numbers. The WMLES is conducted using the Cartesian-grid-based flow solver FrontFlow/Violet Hierarchical Cartesian for Aeronautics Based on Compressible-Flow Equations (FFVHC-ACE). To extend the capability of FFVHC-ACE to transonic flow simulations with shock waves, a hybrid kinetic energy and entropy preserving/upwind scheme is implemented in FFVHC-ACE. To validate the employed simulation framework, the flow around the NASA Common Research Model in the near-cruise condition is simulated. In this case, the surface pressure distributions and force coefficients are reasonably predicted and show the trend of grid convergence. Furthermore, the WMLES at the buffet conditions reproduces the wavy structures of the shock wave (i.e., buffet cells) propagating outboard. The obtained propagation speed of the buffet cells and surface pressure spectra show reasonable agreement with the wind tunnel experiments.