Boundary Layer Ingestion (BLI) engines have the potential to offer significantly reduced fuel burn, but the fan stage must be designed to run efficiently with a distorted inflow. It must also be able to withstand unsteady aerodynamic loads resulting from a non-uniform flowfield. In a multidisciplinary turbomachinery design cycle involving such a complicated flowfield, high fidelity numerical solutions are required. Two high fidelity unsteady Reynolds Averaged Navier-Stokes (URANS) methods for accurate analysis of a Tail Cone Thruster (TCT) transonic fan stage subjected to inlet distortion have been implemented. They are frequency domain based non-linear harmonic (NLH) and full-annulus complete time domain based time marching methods. This paper demonstrates that the relevant parameters required to accurately compute aerodynamic performance of a fan stage in distorted conditions can be accurately modelled with a few harmonics using the NLH method in a fraction of time compared to the full annulus time marching method. However, the complete aerodynamics of distortion transfer across different blade rows of a fan stage can only be analyzed using the time marching solution. Several physical mechanisms which govern the fan response to an inlet distortion and how different distortion profiles impact the aerodynamic performance of this fan stage are also explained.