To provide a fuel cell system capable of surely starting in a short time even after being left unattended over a long time.

A hydrogen substitution valve 8 using a closing valve is a fuel gas discharge means or replacing a hydrogen line with hydrogen, and has an opening area set larger than that of a purge valve 7. When starting, the substitution valve 8 is opened for replacing the gases in a fuel electrode and in a fuel pipe with hydrogen to supply hydrogen to the system from a variable throttle valve 3 at a nearly constant flow rate, and thereby hydrogen substitution (fuel gas substitution) for replacing the inside of a hydrogen line comprising a hydrogen pipe 4, the inside of the fuel electrode and a hydrogen return pipe 6 with newly supplied hydrogen is carried out.

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