This paper presents the application of a recently developed methodology, called Mod-ξ(var), to identify time-varying modal properties of a real-scale base-isolated building subjected to seismic excitation in a shake table and its application for evaluating its modal responses. Modal responses allow for the computation of the empirical response spectrum, obtaining the equivalent isolation layer hysteretic response, and disaggregated modal energy contributions. The methodology enables continuous adjustment of natural frequencies and equivalent damping ratios by applying overlapping short-time windows, providing a refined and smooth representation of the structure’s dynamic and modal responses. This approach is particularly effective for base-isolated systems, where the nonlinear behavior of its isolation layer can lead to significant frequency shifts and damping variations during strong motion phases. Validation of the Mod-ξ(var) methodology was achieved through comparison with experimental data, showing close alignment in response spectra, hysteresis behavior, and total acceleration predictions, with normalized root mean square errors (NRMSE) around 0.18–0.23. The results highlight the method’s capability to track temporal variations accurately, aligning well with previously documented trends in base-isolated structures.