This paper addresses the feasibility and applicability of a semi-active magnetorheological (MR) damper shock isolation system to replace a passive friction damper-based shock isolation system for commercial-off-the-shelf (COTS) equipment. To the end, a shock isolation system using an MR damper was theoretically configured and its mechanical model was developed. From the mechanical model, the governing equation of motion for the shock isolation system with the MR damper was derived and semi-active controls such as skyhook and sliding mode control were formulated based on the derived governing equation of the system. Simulated control responses of the semi-active MR damper shock isolation system with either skyhook, or sliding mode control, were evaluated and compared to those of the passive friction shock isolation system under two different representative shock loads for COTS equipment.