The ballast layer, filled with fine particles like blown sand, is one of the important problems of ballasted railway tracks in desert areas. Blown sand, as a contaminator of ballast layer, increases track stiffness and may cause serious damage to sleepers, pads, rails, and vehicles. In this paper, the effects of increasing track stiffness due to windy sands in the ballast layer and the train induced vibrations due to this phenomenon were studied. Based on field studies in a desert area in Iran, a two-dimensional finite/infinite element model for a railway track with plane strain condition was analyzed using the software ABAQUS, and the track vibrations were examined by changing the values of stiffness of ballast layer. Vibrations caused by the load of train at different distances from the cross-section of track were investigated, and the values of vertical vibration displacement, velocity, and acceleration were calculated. Results show that acceleration values of vertical vibration increase with the increasing of ballast layer stiffness caused by the filling of sand, while the vertical vibration velocity of track and the induced ground displacement decrease. The farther the distance from the source of vibration, the less the displacement, velocity, and acceleration. In addition, the methods for reducing train-induced vibrations were introduced.