This study introduces a Multi-Depth Deflectometer (MDD) combined with a Global Navigation Satellite System (GNSS) which was developed for measuring the deformation of railway slab track layers. We newly designed the MDD with the addition of laser sensor modules for increasing precision in which the MDD head is fixed at the top of the track slab. The MDD/GNSS system can measure the relative deflection between each track layer as well as the total deflection at the top of the track slab, which makes it possible to evade the fixed condition problem of classical MDD. The new MDD/GNSS system was installed at the transition zone between a tunnel entrance and its embankment, which experienced high settlement levels prior to repair. The system was used to monitor whether the repaired concrete track foundation with pressurized cement grouting was stabilized effectively and what track layer position was most unstable so that it had the most influence. The GNSS system was designed and built for computing net settlement at each track layer even when the MDD could not be fixed firmly at the end point, which is a major drawback of classical MDD. The results obtained from MDD and GNSS measurements indicated significant potential in aiding railway track settlement measurements.