A fuel cell system includes a fuel processor; a fuel cell stack; a first water tank; a combustor; a water discharge passage connected to a water drain port formed in the first water tank to discharge the water from inside of the first water tank; a water filling detector configured to detect that at least one of the water drain port and the water discharge passage is filled with water; a water supply unit for supplying the water to the first water tank; and a controller configured to execute a water filling step of supplying the water to the first water, supply the combustible gas to the combustor via the first water tank and cause the combustor to combust the combustible gas, when the water filling detector detects that at least one of the water drain port and the water discharge passage is filled with water.