A fuel injection system that can be used in a diesel engine is provided. The system includes a first accumulator for storing high-pressure fuel and a second accumulator for storing low-pressure fuel sufficiently lower in pressure than the fuel stored in the first accumulator. There is a first two-way electromagnetic valve disposed in a first fuel passage connecting the first accumulator with a fuel injection nozzle. A flow control apparatus controls a flow rate of fuel passing through a second fuel passage connecting a downstream side of the first two-way electromagnetic valve in the first fuel passage with the second accumulator. The flow control apparatus is placed in the second fuel passage. A second two-way electromagnetic valve is placed in a third fuel return passage which connects the fuel injection nozzle with a fuel tank. The second two-way electromagnetic valve switches the fuel injection modes of the fuel from its injection mode to its uninjection mode or vice versa. Also, there is provided a control device for controlling both the first two-way electromagnetic valve and the second two-way electromagnetic valve so that they open and close in response to operating conditions of the engine.