Natural hazards like earthquakes, high winds, and tsunami are a threat all the time for multi-story structures. The environmental forces cannot be clogged but the structures can be prevented from these natural hazards by using protective systems. The structural control can be achieved by using protective systems like the passive, active, semi-active, and hybrid protective systems; but the semi-active protective system has gained importance because of its adaptability to the active systems and reliability of the passive systems. Therefore, a semi-active protective system for the earthquake forces has been adopted in this work. Magneto-Rheological (MR) damper is used in the structure as a semi-active protective system; which is connected to the current driver and proposed controller. The Proportional Integral Derivative (PID) controller and reliable PID controller are two proposed controllers, which will actuate the MR damper and the desired force is generated to mitigate the vibration of the structural response subjected to the earthquake. PID controller and reliable PID controller are designed and tuned using Ziegler-Nichols tuning technique along with the MR damper simulated in Simulink toolbox and MATLAB to obtain the reduced vibration in a three-story benchmark structure. The earthquake is considered to be uncertain; where the proposed control algorithm works well during the presence of earthquake; this paper considers robustness to provide satisfactory resilience against this uncertainty. In this work, two different earthquakes are considered like El-Centro and Northridge earthquakes for simulation with different controllers. In this paper performances of the structure with and without two controllers are compared and results are discussed.