The relatively high maintenance costs of the ballast track are related to the short lifecycle of the ballast layer. The current vertical ballast tamping technology (e.g., Plasser & Theurer, Matisa, etc.) causes high ballast destruction and is neither applicable for unconventional sleepers’ designs nor slab tracks. The side tamping method presents an alternative, ballast saving, and sleeper form independent ballast tamping technology. This paper compares the ballast layer compaction and its resistance to permanent settlements accumulation after the vertical and the side tamping methodologies. Scaled models of ballast layer and tamping units and scaled simulation with discrete element method (DEM) were applied for the comparison. In the laboratory tests, the ballast compaction along the sleeper was estimated using the measurements of elastic wave propagation. The settlements resistance for both tamping methods was estimated under the vibration loading. The tests’ results show 5–7% higher compactness of the ballast layer under the sleeper ends for the side tamping method. The settlement intensity of the ballast layer after the vertical tamping is higher than for the side tamping method. In discrete element modeling, the performed laboratory tests were simulated. The compactness of the ballast bed, as well as the residual stresses, were determined in MATLAB. The side tamping technology provided five times higher residual stresses in the ballast layer below the sleeper than in the case of vertical tamping, which can be explained by the more stable and dense layer resulting from the side tamping ensures higher interlocking between the grains. The simulation of the wave propagation shows an influence of the residual stresses on the wave propagation velocities. The simulated wave propagation velocity was more than two times higher for the side tamping than for the vertical one.