This article deals with the analysis of the accuracy of the geodetic real-time GNSS measurement procedure used in railway operating conditions in the Czech Republic. The purpose was to determine to what extent the operating conditions affect the accuracy of the measurement result and whether an accuracy of standard deviation σx,y = 5 mm in the horizontal plane could be achieved. The use of geodetic GNSS equipment with an IMU unit was also tested. The accuracy obtained in operational conditions is compared with the accuracy obtained on a calibration base using the same measurement procedure. The consistency between the accuracy of the primary system (satellite-based) and the secondary system (terrestrially measured by the traverse method) is also discussed. The analysis includes the issue of residual inhomogeneities of the uniform transformation key when converted to the Czech national coordinate system S-JTSK. It is shown that a homogeneous accuracy in coordinate standard deviation better than σx,y = 5 mm can be achieved. The results indicate that the accuracy under operational conditions is two–three times worse than the accuracy achieved by the same procedure under ideal conditions on a calibration base. This is due to the non-ideal observing conditions, i.e., horizon occlusion by overlays, surrounding vegetation and multipath effects. It has been shown that the effect of multipath can be reduced by repeating short observations 3–4 h apart. Older GNSS instruments using an IMU unit in combination with an electronic compass (eCompass) are at risk of a systematic bias of up to several tens of millimeters, which can be detected by rotating the antenna by 180°. The current uniform transformation key used in the Czech Republic for the conversion of GNSS coordinates into the national system has residual geometric inhomogeneities (p = 0.90 to 10 mm/km, sporadically up to 20 mm/km), which metrologically deteriorate the results of the calculation of the terrestrially measured secondary system inserted into the GNSS measured primary system. Achieving homogeneous accuracy in coordinate standard deviation in a horizontal plane better than σx,y = 5 mm has been demonstrated in non-ideal railway operating conditions with increased risk of multipath. The innovative aspect of the approach used is that it simplifies and thus increases the efficiency of the measurement with respect to the availability of GPS, GLONASS, Galileo and BeiDou satellites, as well as reducing the effect of multipath on the noise by repeating the measurement procedure.