In a system for controlling a general-purpose internal combustion engine having two cylinders each equipped with a throttle valve and a fuel injector, a cooling fan that sucks in and blows air onto the cylinders, there are provided a throttle driver that drives the throttle valve of each cylinder to open/close, an injector driver that drives the injector of each, cylinder to open and a controller that controls operation of the throttle driver and injector driver in such a way that the throttle opening and an amount of fuel to be injected are different for each cylinder, such that an engine speed becomes constant, thereby enabling to obtain desired output characteristics, despite differences of cooling effect among the cylinders due to the cooling fan.