The fuel cell system includes: a fuel cell stack, a hydrogen inlet, a hydrogen outlet, an air inlet, and an air outlet; a hydrogen supply flow path; a hydrogen circulation flow path for circulating gas from the hydrogen outlet to a merging point of the hydrogen supply flow path; a hydrogen pump on the hydrogen circulation flow path; and a gas-liquid separator on the hydrogen circulation flow path. The hydrogen inlet is positioned above the hydrogen outlet, the air inlet is positioned on an upper side of the air outlet, and a direction of connection between the hydrogen inlet and the hydrogen outlet and a direction of connection between the air inlet and the air outlet intersect each other. An upper end of the hydrogen pump is positioned below the stack. The gas-liquid separator is provided at the lowest site of the hydrogen circulation flow path.