Increases in operational train speed have resulted in an elevated probability that dynamic effects will occur inside the railway track and subgrade structure. This is problematic because it causes soil non-linearity, thus resulting in reduced soil stiffness. Therefore, this paper outlines a numerical semi-analytical frequency domain model to compute and analyse non-linear stiffness degradation below railway lines. An equivalent linear approach is used to incorporate non-linear stiffness and damping changes into a thin-layer element frequency-wavenumber domain formulation. The model is validated using published data and then used to analyse non-linearity. It is shown that non-linearity plays an important role in track-ground response, with track displacements increasing significantly in magnitude. It is also shown that the critical velocity can be reduced significantly, which is important because many high speed lines set their dynamic threshold at 70% of the linearly calculated value. Similar findings are made for track velocities and soil strain levels, thus indicating it is vital to consider soil non-linearity when modelling high speed rail track behaviour.