A fuel cell system includes a replacing unit for replacing a gas remaining in the anode of the fuel cell with the anode gas supplied anew by the anode gas supply unit when starting up the fuel cell. The amount of the anode gas is set to be lower, if the operation condition determining unit determines that the last operation was performed in a low-temperature and short-time operation mode. The operation condition determining unit sets the amount of the anode gas so that the gas remaining in the anode can be replaced with the anode gas with an entire anode capacity if the anode was been scavenged while no electro-chemical reaction was progressing in the fuel cell. The present invention can set the amount of anode gas appropriately when starting up the fuel cell.