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Structural assessment for collapse is commonly approached by observing the failure or collapse of systems fully incorporating degradation. Challenges however exist in the performance indicator or damage measure due to compound impacts of uncertainties of external (seismic excitation) and internal (structural properties) characteristics with degradation behavior. To account for the impacts of uncertainties, the state-of-the-art kriging nonlinear autoregressive with exogenous (NARX) model is explored in this study to replicate the response of nonlinear single-degree-of-freedom systems. The generalized hysteretic Bouc-Wen model with internal uncertainties is selected to emulate the stiffness and strength degradation. A probabilistic stochastic ground motion model is introduced to represent the external uncertainties. The global terms of NARX model are selected by least-angle regression algorithm and the kriging model is utilized to surrogate uncertain parameters into corresponding NARX model coefficients. The predictions of kriging NARX models are further compared with that of the polynomial chaos nonlinear autoregressive with exogenous input form model as well as Monte Carlo simulation. The comparisons show that kriging NARX model presents an effective and efficient meta-model technique for uncertainty quantification of systems with degradation.