<p>The mechanical behavior of the train–track system plays a pivotal role in defining relevant operational parameters, such as train speed, comfort, and safety. In sections where the railway subgrade is well compacted, train circulation is smoother and more stable, with lower levels of displacement during operation. However, railway transition zones between embankments and viaducts often show significant stiffness changes, which can lead to differential settlements, larger deflections, and higher maintenance needs over time. This study develops and experimentally calibrates a finite-element computational model to simulate the mechanical response of such transition zones. The model is calibrated using track deflection measurements obtained at only three instrumented locations under trains operating at multiple speeds on an active Brazilian railway. Numerical–experimental comparisons identify the governing parameters affecting track response within the transition region. In addition, a spatial stiffness-variation function is formulated and its parameters are calibrated using the same measurement set. The results allow a more accurate representation of train–track interaction and provide guidance for the design and maintenance of durable, safer railway transition zones.</p>