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Forest roads, haul roads, and especially skid trails have been associated with sedimentation and soil erosion risk. Despite the widespread small shovel harvesting system on steep terrains in South Korea, the subsequent risks of deep (rut depth >5 cm) and compact disturbances, and erosion rates in skid trails are largely unknown. Therefore, the main objectives of this study were to compare the soil erosion rate in each skid trail and predict the total soil erosion rate in a small shovel harvesting area. The soil erosion rate was measured at the plot scale (5 × 3 m) in different skid trail parts (bladed skid trail by small-shovel loader passage, BT; and compacted skid trail CT by carrier passage with construction by a small-shovel loader) using a silt fence experiment. In addition, we investigated the applicability of the Water Erosion Prediction Project (WEPP) model to each disturbance. Among all disturbances, the highest erosion rate (average value of 9.13 ± 0.96 kg m−2 4 months−1) was because of CT. The model predictions were over- and under-estimated and showed particularly poor performance where uncovered soil was exposed (less than 1%) to high machine traffic frequency and excavation. Further, the annual soil erosion rates ranged from 11.59 to 28.94 ton ha−1 year−1. The results suggested that the WEPP model could partially validate the soil erosion results, and further research is still required to improve the accuracy of the model.