A fuel cell system having a fuel cell consuming the hydrogen stored in the high-pressure hydrogen tank as fuel gas, a hydrogen supply line connecting the high-pressure hydrogen tank to the fuel cell, a primary decompressing means provided on the hydrogen supply line, a secondary decompressing means provided in the downstream side of the primary decompressing means on the hydrogen supply line, a hydrogen storage alloy tank saving a hydrogen storage alloy and thermal-exchangeably connected to the fuel cell, a hydrogen pipe connected between the primary decompressing means and the secondary decompressing means, and supplied for hydrogen transfer between the hydrogen supply line and the hydrogen storage alloy tank is provided, and a controlling means for introducing the hydrogen of the first prescribed pressure into the hydrogen storage alloy tank from the hydrogen supply line through the hydrogen pipe during the warm-up of the fuel cell.