Insufficient ballast depth and fouled ballast have been pointed to as causes of settlement and track irregularity. Nondestructive testing methods such as Ground Penetrating Radar (GPR) are a preferred alternative to efficiently evaluate thickness and condition of railroad ballast. Data collected using commercial GPR devices show significant noise around and under sleepers. Furthermore, GPR data need attentive preprocessing and filtering of unnecessary noise before main analysis. In this study, to eliminate noise due to the sleeper, a GPR device with a transmitter and a receiver in a separate box is developed. In addition, an algorithm that can automatically detect the thickness of the ballast layer is also proposed. Comparison between data from the developed device and from a conventional device shows that the developed device can effectively eliminate noise. The trial pit measurements show that the proposed algorithm with the developed GPR device can accurately determine the thickness of ballast.