A railway line needs to pass over necessary civil structures such as pipes, bridges and culverts. Because these structures are made of stiff materials such as concrete and steel, changes in track stiffness exist at the transition zone between the railway embankment and stiff structures. As a consequence, the dynamic stresses at backfills and interaction forces between the train body and the track are amplified at the transition zones. The field observation shows a rapid track degradation rate at the transition zones where frequent maintenance work has to be conducted. It is therefore an important subject receiving massive attention from academia and industry. The role of culverts in the dynamic performance of transition zones is studied aiming to better guidelines on transition zone performance. Numerical studies are conducted with a Finite Element Method using a commercial program Plaxis, and a linear elastic material model is used for transient dynamic analysis. The validation study has been performed by comparing the numerical and observation data regarding rail vertical displacements and their frequency content. The parameter study has been performed on culvert depth, culvert size, culvert shape and culvert foundation. Two different transition zone configurations are considered for deep and shallow culverts. The relatively fast wave induced by train loads and small vertical displacements are found around the culvert due to its high stiffness. Much larger vertical stresses are observed in the ballast and subgrade layers at the transition zone around the culvert. Nearly two times dynamic vertical stresses are observed around the culvert at the subgrade surface from shallow culvert configuration. The large dynamic vertical stress can account for the frequent track degradation adjacent to the culvert. Therefore, it is recommended to calculate dynamic stresses when designing railway lines. The culvert foundation, a structure normally constructed behind the culvert, plays a negligible effect on track displacement (track stiffness). The vertical stress distribution around the culvert is changed slightly with the culvert foundation. It could improve drainage and permanent deformation issues, which has not been studied here. The culvert depth, the distance of the culvert’s top surface to the ballast layer, is an essential parameter to track dynamic responses. Larger rail displacements and dynamic stresses are found with smaller culvert depths. The effect is especially evident with a shallow culvert. For example, when the culvert depth equals 0.1 m, a sharp increase in rail displacement and dynamic stress at the ballast layer is found. Therefore, more effort and higher requirements are needed for the transition zone for shallow culverts, such as using longer transition zones. To study the effect of culvert sizes on railway dynamic responses, four culvert sizes are used. Its size is increased by four times for the rectangular culvert. Its effect on rail displacements is very minor. A slight increase in dynamic stresses is found with the increase in culvert size. Three culvert shapes (an arch culvert, a pipe culvert and a rectangular culvert) are used to study its shape effect, in which their inside space and thickness are kept the same. A negligible impact is found on the track settlement and dynamic stresses at ballast and subgrade layers. However, the stress distribution in the culvert structure is distinct for three culverts. Therefore, the culvert shape may be determined by economical and construction factors without considering of railway dynamics.