An object of the present invention is to provide a fuel cell system configured to be able to suppress loads imposed on a liner caused by gas filling, as well as a method for supplying fuel gas in the fuel cell system, and a mobile body. The fuel cell system includes a fuel cell, a tank which includes a liner and a reinforcement layer formed on an outer peripheral surface of the liner and in which fuel gas is stored, an adjustment device configured to adjust a supply amount of fuel gas to be fed from the tank to the fuel cell, an information acquisition section configured to acquire information on a pressure and a temperature in the tank, a calculation section configured to calculate a gap amount between the liner and the reinforcement layer based on information acquired by the information acquisition section during operation of the fuel cell system, and a decision section configured to decide whether or not to limit the supply amount based on the calculated gap amount.