A plant control system controls a plant modeled as a discrete-system model including an element relative to a response delay of the plant and an element relative to a dead time of the plant. The plant control system includes an actuator for generating an input to the plant, a first detector for detecting an output from the plant, and a second detector for detecting the input to the plant. An estimator generates data representing an estimated value of an output of the first detector after the dead time, based on data representing the output of the first detector and data representing an output of the second detector. A manipulated variable determining unit determines a manipulated variable which determines the input to the plant, based on the estimated value, represented by the data generated by the estimator, of the output of the first detector after the dead time. The input to the plant from the actuator is controlled such that the output from the first detector will be equalized to a predetermined target value.