A fuel cell system includes: a fuel cell including an inlet and an outlet; first and second injection devices injecting purge gas; a gas-liquid separator separating liquid water from the purge gas discharged from the outlet and causing the liquid water to flow out; a discharge valve discharging the liquid water flowing out to an outside; an ejector including: an inflow port and an outflow port for the purge gas; a first connection path between the outflow port and the inlet; an introduction path introducing the purge gas injected from the second injection device into the first connection path without flowing through the ejector; a second connection path between the gas-liquid separator and the outlet; a third connection path connected between the gas-liquid separator and the inflow port, and extending vertically upward from the gas-liquid separator; and a controller.