Through the formulation of a mathematical model from time series records, the poles and zeros can be evaluated for a dynamic system. This paper identifies the dynamic characteristics of a strengthened stone masonry prototype building using the splint-and-band technique. A two storied stone masonry building left after a demonstration test was subject to a series of impact excitations in the impact testing facility (shock table) and time series records were taken using three triaxial accelerometers. A series of impacts were deployed, and the vibration frequencies were estimated using the state space system identification technique implemented through the Numerical Algorithms for Subspace State Space System Identification (N4SID) method. After observing a significant damage aggravation, the vibration frequency along the longer wall direction was reduced to 3.38 Hz from 7.42 Hz, whereas the frequency along the short wall direction was reduced to 4.62 Hz from 5.82 Hz. The reduction in the vibration frequencies is attributed to damage induced by the impact loading. Since ambient vibration cannot excite the higher modes in a structure, blind system identification is often challenging. A further challenge arises while estimating the damping ratio since a free vibration response of a structure cannot be achieved through ambient vibration measurements. To overcome this challenge, a series of impacts were imposed, and the damping ratio was estimated using the free vibration response of the building. The damping ratio for the tested building is found to be 1.1%. Numerical analyses often use a higher value of damping ratio than the one estimated from the free vibration response. Since there is no unanimous agreement regarding the damping characteristics of stone masonry constructions, the results reported in this study could provide a rational basis for numerical modeling. This paper also presents sequential frequency reduction adhering to each impact. Some remarks on future instrumentation and output-only system identification are also provided.