A gas supply system that supplies a gas after making confluence of the gas flows from gas containers includes: a supply pressure detector that detects supply pressure of the gas following the confluence; and a controller that permits a gas supply-destination apparatus to be activated if the supply pressure detected after an elapse of a determination time from a start of the gas supply is greater than or equal to a threshold pressure, and that prohibits the apparatus from being activated if the supply pressure is less than the threshold pressure. The controller uses a first determination time as the determination time if it is determined that internal pressures that are the gas pressures in the containers are not imbalanced between the containers, and uses a second determination time that is longer than the first as the determination time if it is determined that the internal pressures are imbalanced.