Abstract: In a fuel injection system for an engine, a first controller calculates circuit rotational angle of a crankshaft on the basis of reference pulses and scale pulses from a detector for detecting rotation of the crankshaft. The first controller outputs a drive pulse representative of a closing command moving an electromagnetic valve to a closed position, at a timing with reference to the current rotational angle, to control a period, within which the valve is in the closed position, during forward stroke of a plunger. A second controller intermittently outputs drive pulses representative of the closing command, at an initial stage of engine start-up, independently of the crankshaft rotational angle. A time duration of each drive pulse from the second controller is shorter than a time duration required for the plunger forward stroke, and a period within which each drive pulse is not outputted from the second controller is also shorter than the time duration required for the plunger forward stroke.