Crosswind can reduce the operability of an aeroengine significantly at static or near static operating conditions. Computational fluid dynamics predictions of the flow at crosswind conditions will play an important part in future designs, however, accurate numerical predictions of the flow within the intake remain challenging even for simulations of cases with intake only. The main objective of this paper is to demonstrate the importance of numerical setup and to determine an optimal computational model for crosswind investigations that can be used by other researchers. By considering the flow to be inherently unsteady, the influence of inlet and exit boundary conditions, and grid sensitivity is studied by using unsteady Reynolds-average Navier–Stokes (URANS) simulations. Numerical predictions of the time-averaged intake pressure recovery (IPR) and the motion of the vortex on the ground are compared against the existing experimental data. The results show that for an intake under crosswind, the ground vortex that forms under the intake and the in-duct separation, when present, exhibit unsteady behavior that become stronger as the crosswind velocity is increased. The steady-state simulation is only representative at lower crosswinds. The intake flow separation and ground vortex predictions are influenced by the inlet boundary layer profiles. Moreover, acoustic reflection was observed at the intake exit boundary which propagates upstream, creating artificial unsteady frequencies in IPR. The reflection is generated from the use of uniform boundary conditions at the intake exit and is not dissipated in the grid due to the long wavelength; this can be mitigated by using a choked nozzle at the intake exit. Acoustic reflection was also observed at the far-field exit boundary. These reflections are caused from interaction of trailing vortex and far-field boundary.