Provided is a method of operating a fuel cell system equipped with a fuel cell stack, a liquid hydrogen storage unit configured to store liquid hydrogen, a boil-off gas recovery unit configured to recover boil-off gas generated from the liquid hydrogen storage unit, and a hydrogen concentration estimation unit configured to estimate the hydrogen concentration at a hydrogen electrode in the fuel cell stack in a standby state, the method including: in a case in which a hydrogen concentration at a hydrogen electrode in the fuel cell stack in a standby state has become less than a predetermined value, supplying boil-off gas recovered by the boil-off gas recovery unit to the hydrogen electrode in the fuel cell stack.