In recent years, the vehicle-based indirect Structural Health Monitoring (iSHM) method has been increasingly used to identify the dynamic characteristics of railway bridges during train crossings, and it has been shown that this method has several advantages compared to traditional SHM methods. A major advantage is that sensors are just mounted on the vehicle, and no sensors or data acquisition systems need to be installed on the railway bridge. In this paper, the application of the vehicle-based iSHM method is demonstrated numerically and experimentally for determining the natural frequencies of railway steel bridges during train crossing. The coupled linear equations of motion of the train-bridge multi-body system are derived, and train crossing simulations are conducted numerically, considering different train speeds. Three different railway bridges are considered, and the train-induced vibration responses are calculated for both the train multi-body system and the railway bridge models. Different representative evaluation points are chosen for the wheelsets, bogies, and car bodies of the considered vehicle. To calibrate the numerical model, the resonance frequencies of an existing single-span steel bridge are measured in situ by the application of forced vibration tests. Besides the executed in situ measurements of the bridge, the considered crossing vehicle is also instrumented with several accelerometers at the wheelsets, bogies, and car bodies, and the vibration responses of both the bridge and the crossing vehicle are measured simultaneously during the duration of several train crossings with different train speeds. The recorded vibration responses are analyzed in the frequency domain and compared with numerical simulation results. It is shown that the first bending frequency of the considered railway bridge can be clearly identified from the computed frequency response spectra and that the vehicle-based iSHM method provides a promising tool for identifying the dynamic characteristics of railway bridges.