A common issue for Canadian railway operators is the development of localized frost heave near railway culverts, which leads to nonuniform deformation of the track surface and degradation of the track geometry, damages the track component, and affects the quality of rides in railway operations. Frequent maintenance including placing wooden shims between rail and ties and often the reduction of train speeds are required to ensure safe operating conditions. Given the future expected climate patterns, freeze–thaw cycles are anticipated to become more frequent, and therefore, a greater understanding of their effect on the changing ground thermal regime under railway embankments is essential. This paper investigates the effects of culverts and insulation layers on changing the temperature regime of the ground during the winter–spring period through numerical modeling in TEMP/W (version 2019) two-dimensional (2D) and three-dimensional (3D) software. The model was calibrated using actual field measurements collected from an instrumented section of the track that has suffered from frost heaves at the proximity of a culvert. Using the results from 2D simulation, the effect of culverts on extending the frost zone, in both horizontal and vertical directions, was quantified. In addition, the effects of shape, installation depth, and the number of culverts on the frost penetration depth were discussed. Using TEMP/W 3D results, the most appropriate configuration to install the culverts was studied to minimize frost penetration.