The invention relates to a method and an apparatus for manufacturing a fuel storage tank used for a fuel storage system and provided with a liner and an internal bag. Specifically, provided are an apparatus and a method for manufacturing a fuel storage tank of a fuel cell system which is used for storing various pressure fluids and reducing separate permeation characteristics during various temperature and pressure cycles. The fuel storage tank comprises a liner formed to define an internal cavity, a boss connected to the liner, a reinforcing structure formed around a portion of the liner around and the boss, and a permeation bag attached to a first fixing part and inserted into the inner cavity of the liner. The first fixing part is coupled to the boss, and a second fixing part is mounted to the boss and adjacent to the first fixing part so that non-permeable fluids between the permeation bag, the liner and the boss are connected.