The objective of the present study is to characterise the dynamic response of ballasted railway embankments subject to high-speed train loads, for the track conditions with and without inclusions of geofoam in-filled trenches next to the embankments for passive isolation of ground vibrations. Full-scale models of the ballasted railway track sections were developed for the simulation of high-speed train transit. Although vibration isolation trenches have been characterised as a suitable method for attenuation of ground-borne railway vibrations propagating away from the track, the results from the present study signify that the embankments supporting the railway track are subject to augmented levels of vibrations, due to reflection of ground vibrations from the soil–trench interface back into the embankment. In-filling of trenches with EPS (expanded polystyrene) geofoam of high buffer stiffness results in stronger reflection of ground vibrations back into the railway embankment. Augmented levels of track vibration are also estimated, when geofoam with higher densities are used for in-filling the trench. Deployment of vibration isolation trenches with higher depths result in stronger reflection of ground vibrations as well, especially when the trench is deployed at locations farther from the track. In general, amplification of vibrations in the railway embankment is higher when the trains transit at faster speeds. Reflection of vibrations by the passive vibration isolation trenches is inevitable, and hence, it is recommended that rail pads or under-sleeper pads shall be used in conjunction with the passive trenches for limiting the amplification of vibrations in the embankment.