This paper presents a semi-active seat suspension with a magneto-rheological (MR) fluid damper, which is applicable to commercial vehicles such as a large size of truck. A cylindrical MR seat damper is designed and manufactured by incorporating Bingham model of MR fluid. After evaluating field-dependent damping characteristics, the controllability of the damping force is experimentally demonstrated in time domain by implementing PID controller. A semi-active seat suspension system is then constructed and its governing equation of motion is derived. A skyhook control scheme is formulated in order to reduce vibration level at the driver's seat. The controlled responses such as acceleration transmissibility are evaluated in frequency domain. In addition, performance characteristics of a full-car model installed with the proposed MR seat suspension are evaluated via hardware-in-the-loop simulation (HILS).