In a previous study, the authors proposed a hydrogen generation system fueled by sodium tetrahydroborate. However, the hydrogen generated by this system at the purging operation of a fuel cell experiences pressure fluctuation. To solve this issue, this paper proposes a purge compensation method. In this method, the amount of fuel which can generate the same amount of the hydrogen released at purging is added to the amount output by the pressure controller. In addition, experiments were conducted to show that the proposed method can reduce the pressure fluctuation caused by purging.