A valve actuator for a combustion engine has a movable member for collaborating with a stem of a valve, and an electromagnetic device with a permanent magnet associated with a resilient device for moving the movable member between an extreme valve-closed position and an extreme valve-open position. A method of controlling the valve actuator has the steps of determining a clearance range between the movable member and the valve stem during the movement of the movable member between the extreme closed and open positions, determining, in the clearance range, intermediate positions reached by the movable member as a function of different values of an electrical control parameter of the electromagnetic device, and using positional feedback control to control the electromagnetic device, using one of the intermediate positions as a setpoint value, according to the desired performance of the actuator.