In this study, a real-time damage detection method using output-only acceleration signals and artificial neural networks (ANN) is developed to monitor the occurrence of damage and the location of damage in structures. A theoretical approach of an ANN algorithm that uses acceleration signals to detect changes in structural parameters in real-time is newly designed. Cross-covariance functions of two acceleration responses measured before and after damage at two different sensor locations are selected as the features representing the structural conditions. By means of the acceleration features, multiple neural networks are trained for a series of potential loading patterns and damage scenarios of the target structure for which its actual loading history and structural conditions are unknown. The feasibility of the proposed method is evaluated using a numerical beam model under the effect of model uncertainty due to the variability of impulse excitation patterns used for training neural networks. The practicality of the method is also evaluated from laboratory-model tests on free-free beams for which acceleration responses were measured for several damage cases.