A method of controlling an internal combustion engine having an electromagnetically actuated intake valve for a cylinder. The controlling method comprises (a) forming first and second control regions in accordance with an engine speed of the engine, the first control region being higher in engine speed than the second control region; (b) calculating opening and closing timings of the intake valve in synchronism with a first cylinder synchronous signal in the first control region, the first cylinder synchronous signal being generated in synchronism with a stroke of an operating cycle of a cylinder; (c) calculating the opening and closing timings of the intake valve in synchronism with a second cylinder synchronous signal in the second control region, the second cylinder synchronous signal being generated in synchronism with the stroke of the operating cycle of a cylinder and after generation of the first cylinder synchronous signal; and (d) controlling an amount of intake air to be supplied to the cylinder in accordance with the calculated opening timing of the intake valve.