A fuel cell system is provided in which the amount of a reaction product discharged outside the system can be reduced, the reaction product, such as water, being formed by the electrochemical reaction of a fuel cell. The fuel cell system includes a fuel cell power generation apparatus and a fuel cartridge which is detachable from a fuel cell. The fuel cell power generation apparatus includes a case containing a fuel cell therein, an air intake port provided in the case, and an emitted material discharge port provided in the case. The air intake port and the emitted material discharge port are arranged in different positions of the case. The fuel cartridge includes a fuel storage unit storing fuel, a fuel supply port supplying the fuel to the fuel cell, and a removal unit which removes water discharged from the fuel cell.