In this paper, a two-stage time-domain output-only damage detection method is proposed with a new energy-based damage index. In the first stage, the random decrement technique (RDT) is employed to calculate the random decrement signatures (RDSs) from the acceleration responses of a simply supported beam subjected to a moving load. The RDSs are then filtered using the Savitzky–Golay filter (SGF) in the second stage. Next, the filtered RDSs are processed by the proposed energy-based damage index to locate and quantify the intensity of the possible damage. Finally, by fitting a Gaussian curve to the damage index resulted from the non-damage conditions, the whole process is systematically implemented as a baseline-free method. The proposed method is numerically verified using a simply supported beam under moving sprung mass with different velocities and damage scenarios. The results show that the proposed method can accurately estimate the damage location/quantification from the acceleration data without any prior knowledge of either input load or damage characteristics. Additionally, the proposed method is neither sensitive to noise nor velocity variation, which makes it ideal when obtaining a constant velocity is difficult.