A fuel cell system includes: first and second injectors; first and second ejectors; a first circulation passage configured to circulate anode gas that has passed the first ejector between the first fuel cell and the first ejector; a second circulation passage configured to circulate the anode gas that has passed the second ejector between the second fuel cell and the second ejector; a communication passage communicating with the first and second circulation passages; a switching valve configured to switch the communication passage to a communication state where the first and second circulation passages communicate with each other or to a cutoff state where the first and second circulation passages are cut off; and a controller configured to scavenge the first fuel cell by injecting the anode gas with the first injector, while the first fuel cell stops power generation in the communication state.