This study introduces an approach for probabilistic seismic performance estimation, which focuses on the probability of intensity measures exceeding a specified value based on engineering demand parameters. Conventional methods face challenges owing to the increase in computational costs associated with the uncertainties in earthquake scenarios. To address this, we use high‐fidelity (HF) and low‐fidelity (LF) model data to develop a multilevel hierarchy of surrogate models, which improves the simulation‐based probabilistic estimation. However, designing a reliable LF model and ensuring the accuracy of the surrogate model hierarchy remains challenging. Herein, we present a multi‐fidelity Monte Carlo (MFMC) predictor combined with a conventional surrogate model to improve probabilistic seismic performance estimation, thereby leveraging LF model efficiency and HF data accuracy for unbiased results. We addressed the challenge of constructing a suitable LF model by using a surrogate model trained from limited HF data. The MFMC predictor improves the accuracy of probabilistic analysis than the surrogate models trained from limited HF data. Further, the automatic relevance determination method is introduced to select the most appropriate inputs for the surrogate model. A case study featuring a special moment‐resistant frame, subject to uncertainties from both ground motion and structural properties, illustrates the efficiency of the method. A LF model is developed using the Kriging method, followed by the construction of the MFMC predictor for probabilistic analysis, thereby leveraging both limited HF and numerous LF data. Comparing the exceedance probability curves obtained from the MFMC predictor with those from direct Monte Carlo simulations and conventional Kriging showed that our proposed method offers a promising tool for probabilistic seismic performance estimation under uncertainty.