A fuel cell system includes: a first fuel cell stack; and a second fuel cell stack with lower output voltage than the first fuel cell stack, a pre-switching stack configured by the first fuel cell stack or the second fuel cell stack, a step-up stack configured by the first fuel cell stack or the second fuel cell stack, a post-switching stack configured by at least the first fuel cell stack, and steps up voltage of the step-up stack with the pre-switching stack connected to the load and then switches to a connection state where the post-switching stack is connected to the load.