This paper presents signal filtering methods that can be effectively applied to train detection systems based on the axle counter systems that are currently in operation for train detection and provide information on the unoccupied status of railway tracks and turnouts. Signals from the wheel detectors contain noise, may be impulsive and time-varying, which means that even for the same train, the signals from the following wheels may be different. A problem appears when already homologated hardware (axle counter system) is working in a harsh environment, exposed to disturbances whose parameters significantly exceed standard thresholds. Despite this, the system must continue to provide reliable information. The authors present research on the application of such filters as median, Savitzkey-Golay, and moving average which can be implemented in the equipment currently in use under specific constraints (e.g., limited computational resources). The research results show that appropriately adjusted filters, for example, in terms of type and window size, increase the signal quality and thereby provide reliable information about passing trains, as well as enhance the availability and safety of the axle counter system performance.