In a fuel injection system of an internal combustion engine in which a first fuel, which has a property to inhibit the adsorption of exhaust gas components by an exhaust gas purification catalyst, and the second fuel, which has a property not to inhibit the adsorption of the exhaust gas components by the exhaust gas purification catalyst, are able to be selectively used, the present invention has a task to decrease an amount of consumption of the second fuel in a suitable manner. In order to solve this task, the fuel injection system of an internal combustion engine according the present invention is constructed such that the second fuel is first supplied to the internal combustion engine when the exhaust gas purification catalyst is in a cold state, and a change from the second fuel to the first fuel is then made before the exhaust gas purification catalyst subsequently rises in temperature to an activation temperature thereof.