A controller for a variable valve actuation mechanism applied to an internal combustion engine, wherein the engine includes a plurality of cylinders, a plurality of intake valves each provided in one of the cylinders, and a variable valve actuation mechanism (600; 610), which changes valve actuation of the intake valves, and the engine is operable in a cylinder deactivation mode, which keeps the intake valves of some of the cylinders closed, the controller comprising: a control section that controls the valve actuation in accordance with an engine output requirement, wherein even during execution of the cylinder deactivation mode, the intake valve of an operating one of the cylinders is opened and closed, the control section executes an intake amount correction process, which controls the valve actuation of the operating cylinder such that, when the internal combustion engine is reactivated from the cylinder deactivation mode, opening duration of the intake valve of the operating cylinder is temporarily increased as compared to the opening duration in a case in which the valve actuation of the operating cylinder is controlled in accordance with the engine output requirement during the cylinder deactivation mode, when overlap occurs in opening duration of the intake valves between the cylinders by controlling the valve actuation in accordance with the engine output requirement at reactivation from the cylinder deactivation mode, the control section executes the intake amount correction process such that the intake air amount of the operating cylinder is increased as compared to a case in which the valve actuation is controlled in accordance with the engine output requirement during the cylinder deactivation mode, and the control section terminates execution of the intake amount correction process after a first combustion of air-fuel mixture after the reactivation from the cylinder deactivation mode in the cylinder reactivated from the cylinder deactivation mode. a control section that controls the valve actuation in accordance with an engine output requirement, wherein even during execution of the cylinder deactivation mode, the intake valve of an operating one of the cylinders is opened and closed, the control section executes an intake amount correction process, which controls the valve actuation of the operating cylinder such that, when the internal combustion engine is reactivated from the cylinder deactivation mode, opening duration of the intake valve of the operating cylinder is temporarily increased as compared to the opening duration in a case in which the valve actuation of the operating cylinder is controlled in accordance with the engine output requirement during the cylinder deactivation mode, when overlap occurs in opening duration of the intake valves between the cylinders by controlling the valve actuation in accordance with the engine output requirement at reactivation from the cylinder deactivation mode, the control section executes the intake amount correction process such that the intake air amount of the operating cylinder is increased as compared to a case in which the valve actuation is controlled in accordance with the engine output requirement during the cylinder deactivation mode, and the control section terminates execution of the intake amount correction process after a first combustion of air-fuel mixture after the reactivation from the cylinder deactivation mode in the cylinder reactivated from the cylinder deactivation mode.