Ground penetrating radar (GPR) is a popular technology for inspecting railway ballast layer, mainly on the ballast fouling level. However, different GPR antennas with different frequencies are suitable for different inspection emphasis and diverse railway lines (weather and sub-structure). In addition, the full-scale track model (with subgrade) for experimental tests was not seen in earlier studies. For further application of GPR in China, the GPR inspections (with 400 MHz, 900 MHz and 2 GHz antennas) were performed on a 30 m long full-scale track and three railway lines (different weather and sub-structure). Results show that ballast layer inspection should be performed mainly with the 2 GHz antenna and supplemented by the 400 MHz and 900 MHz antennas. The weather has great influence on the results of GPR inspection. This study is helpful for supplementing the guidance of ballast layer inspection with GPR.