In a system for controlling an engine having an input u, there are provided with applying means (vibration signal) for applying a component p that changes at a predetermined cycle to the plant, a Washout Filter for calculating a parameter h based on an output y of the plant, a finite interval integrator for integrating a value j obtained by multiplying the calculated parameter h by the applied component p in an interval of integral multiple of a cycle of the component p, and an infinite interval integrator, etc. for calculating the input u based on the integrated value g obtained by the integration. Owing to this configuration, it becomes possible to provide a system that can optimize the output y, while preventing the resonance of the control system.