To reduce regular combustion variations across combustion cycles, an engine control apparatus includes: an engine that has cylinders inside of which gas exchange is performed by opening and closing an intake valve and an exhaust valve for each cylinder, and that is operated by causing a plurality of the cylinders to sequentially execute combustion cycles; a combustion control device that is attached to the engine, and controls combustion in each of the plurality of cylinders; and a controller that controls the operation of the engine by outputting a control signal to the device, wherein the controller, before combustion in each of the plurality of cylinders, estimates state quantities of the cylinder based on a plant model of the engine which indicates regular combustion variations across the combustion cycles, and outputs to the combustion control device the control signal, which has been corrected based on the estimated state quantities.