Although there have been many implementations of Global navigation satellite system (GNSS) in rail transport systems, the integrity assurance of GNSS positioning is still not highly concerned by the users. Integrity is a significant issue for specific safety-relevant GNSS railway applications, especially the railway signaling system which requires a critical safety level. Classical integrity monitoring solutions require an acceptable satellite visibility level to carry out Fault detection and exclusion (FDE), and this restriction leads to a degraded availability of FDE and final position computation. In order to break the limitation by satellite visibility, a consistency check method for FDE is proposed based on the virtual satellite pseudorange data, which is established based on the track database. Results from simulations show that the presented method can detect and exclude different types of faults effectively. Compared with classical residualbased GNSS integrity monitoring algorithm, the presented method achieves a higher FDE availability and makes better use of the satellite measurements even under the limited GNSS observing conditions.