A fuel cell system includes a fuel cell, auxiliary devices, an auxiliary device controller, a secondary battery, a current sensor, a voltage sensor, and a diagnosis controller. In an output stop state where the fuel cell does not output electric power, the auxiliary device controller performs a residual water scavenging process of scavenging water remaining in the fuel cell to outside of the fuel cell system by driving the auxiliary devices using electric power supplied from the secondary battery and supplying the gas to the fuel cell. The diagnosis controller diagnoses the secondary battery using a current integrated value that is obtained by integrating amounts of current supplied from the secondary battery in a predetermined voltage range of a discharge voltage of the secondary battery that changes in response to discharge when electric power is supplied to the auxiliary devices by performing the residual water scavenging process.