Finite element (FE) model updating is a useful tool for global damage detection technique, which identifies the damage of the structure using measured vibration data. This paper presents the application of a finite element model updating method to detect the damage of a small-scale reinforced concrete building structure using measured acceleration data from shaking table tests. An iterative FE model updating strategy using the least-squares solution based on sensitivity of frequency response functions and natural frequencies was provided. In addition, a side constraint to mitigate numerical difficulties associated with ill-conditioning was described. The test structure was subjected to six El Centro 1942 ground motion histories with different Peak Ground Accelerations (PGA) ranging from 0.06 g to 0.5 g, and analytical models corresponding to each stage of the shaking were obtained using the model updating method. Flexural stiffness values of the structural members were chosen as the updating parameters. In model updating at each stage of shaking, the initial values of the parameter were set to those obtained from the previous stage. Severity of damage at each stage of shaking was determined from the change of the updated stiffness values. Results indicated that larger reductions in stiffness values occurred at the slab members than at the wall members, and this was consistent with the observed damage pattern of the test structure.