The disclosure relates to a fuel cell system. The fuel cell system includes a fuel cell module, fuel and oxidizing gas. The fuel cell module includes a container and a membrane electrode assembly located on the container. The container includes a housing and a nozzle connected to the housing. The container defines a number of through holes located on the housing and covered by the membrane electrode assembly. The membrane electrode assembly includes a proton exchange membrane having a first surface and a second surface opposite to the first surface, a cathode electrode located on the first surface and an anode electrode located on the second surface.