Two very dense seismographic arrays were deployed in a seismically active area in Greece to incorporate the difference in amplitude and phase between two stations located within the dimension of a structure. The spatial variability in seismic ground motion is generally attributed to the wave passage effect, the incoherence effect, and the local site effect. It can cause severe damage on lifeline structures. This article studies the behavior of a reinforced concrete 2D frame structure subjected to differential seismic excitation at the supports. Both linear and nonlinear finite multifiber element models of the seismic behavior of this structure are used. The nonlinear behavior of the structure, under these different cases, displays different damage patterns and maximum displacements. This study allows evaluating the uncertainty that can be propagated through the finite element model, aiming at reducing variability for structural design purposes.