Fractional-order models provide a powerful framework for capturing memory-dependent and viscoelastic dynamics in mechanical systems, which are often inadequately represented by classical integer-order characterizations. This study addresses the identification of dynamic parameters in both single-degree-of-freedom (1-DOF) and three-degree-of-freedom (3-DOF) Duffing oscillators with fractional damping, modeled using the Grünwald–Letnikov characterization. The 1-DOF system includes a cubic nonlinear restoring force and is excited by a harmonic input to induce steady-state oscillations. For both systems, time domain simulations are conducted to capture long-term responses, followed by Fourier decomposition to extract steady-state displacement, velocity, and acceleration signals. These components are combined with a GL-based fractional derivative approximation to construct structured regressor matrices. System parameters—including mass, stiffness, damping, and fractional-order effects—are then estimated using pseudoinverse techniques. The identified models are validated through a comparison of reconstructed and original trajectories in the phase space, demonstrating high accuracy in capturing the underlying dynamics. The proposed framework provides a consistent and interpretable approach for frequency domain system identification in fractional-order nonlinear systems, with relevance to applications such as mechanical vibration analysis, structural health monitoring, and smart material modeling.