Provided is a fuel cell system which can perform sufficient scavenging during a current system operation even if required sufficient scavenging during the previous system stop is not performed. When a control device detects that a system start command is input and a low temperature mode flag is turned “ON”, the control device compares a measured impedance during the previous system stop stored in a measured impedance memory to a low temperature start target impedance It stored in a reference impedance memory, to judge whether or not a scavenging process performed during the previous system stop has been insufficient. When the control device judges that the scavenging process is insufficient, an immediate warm-up operation is executed during the current system operation to immediately raise the temperature.