The condition of the ballast is a critical factor affecting the riding quality and the performance of a track. Fouled ballast can accelerate track irregularities, which results in frequent ballast maintenance requirements. Severe fouling of the ballast can lead to track instability, an uncomfortable ride and, in the worst case, a derailment. In this regard, maintenance engineers perform routine track inspections to assess current and future ballast conditions. GPR has been used to assess the thickness and fouling levels of ballast. However, there are no potent procedures or specifications with which to determine the level of fouling. This research aims to develop a GPR analysis method capable of evaluating ballast fouling levels. Four ballast boxes were constructed with various levels of fouling. GPR testing was conducted using a GSSI (Geophysical Survey Systems, Inc.) device (400, 900, 1600 MHz), and a KRRI (Korea Railroad Research Institute) GPR device (500 MHz), which was developed for ballast tracks. The dielectric permittivity, scattering of the depth (thickness) values, signal strength at the ballast boundary, and area of the frequency spectrum were compared against the fouling level. The results show that as the fouling level increases, the former two variables increase while the latter two decrease. On the basis of these observations, a new integrated parameter, called a ballast condition scoring index (BCSI), is suggested. The BCSI was verified using field data. The results show that the BCSI has a strong correlation with the fouling level of the ballast and can be used as a fouling-level-indicating parameter.