Transition zones of railway tracks are intended to provide a smooth transition of the riding train, minimizing the effect of the discontinuities that exist along the track. When a train rides from an embankment onto a stiff structure, such as a bridge, tunnel or culvert, an abrupt change in the support stiffness occurs possibly inducing differential settlements. This in long term can yield to the degradation of the tracks and foundations in the transition zones. The differential settlement is especially problematic for high speed rail infrastructure as the "bump" at the transition is accentuated at high speeds. A number of techniques have been proposed or implemented to provide gradual stiffness transition at the problem zones, such as methods to ensure gradually changing pad stiffness, application of long sleepers or installation of auxiliary rails in the transition zone. The problems associated with the transition zones require a complex analysis. For efficient modeling of the mechanisms resulting in gradual line deteriorations in the transition zones the understanding of the 3D and dynamic effects associated with the problem seems to be essential. To enhance our understanding regarding the problem a 3D numerical model has been developed and presented for time domain analysis.