An operation method of a fuel cell system includes providing a turbo pump to supply an oxidant gas to a fuel cell to generate power through a reaction between a fuel gas and the oxidant gas. A branch valve to regulate a flow rate of the oxidant gas which flows through a branch passage that connects an oxidant gas supply passage and an oxidant off-gas discharge passage is provided. The turbo pump and the branch valve are controlled to regulate a flow rate of the oxidant gas to be supplied to the fuel cell in an extremely low power generation mode in which an extremely low generation power is requested. The extremely low generation power is less than or equal to a predetermined generation power corresponding to a minimum flow rate of the oxidant gas that is supplied by the turbo pump.