A fuel cell system includes a three-way valve installed on a hydrogen supply line between a fuel cell stack and a hydrogen tank, a first hydrogen supply valve installed on a first hydrogen supply line branching off by the three-way valve and configured to variably adjust a hydrogen supply pressure, a second hydrogen supply valve installed on a second hydrogen supply line branching off by the three-way valve and configured to adjust the hydrogen supply pressure to a constant pressure, and a controller configured to control a supply of hydrogen to one of the first hydrogen supply line and the second hydrogen supply line according to a state of the hydrogen tank while the fuel cell stack operates.