An apparatus and method of controlling a motor driven steering system may selectively perform a motor current control of the motor driven steering system for reducing motor noise according to a present motor-applied current applied to a steering motor of the motor driven steering system when it is determined from vehicle speed information or wheel speed information detected by a first sensor that a vehicle is currently in a stopped state and it is determined from steering angle information detected by a second sensor that a steering wheel is currently in a steering wheel holding state.