A method of manufacturing a fuel cell which enables organic matter of both an anode thereof and a cathode thereof to be removed efficiently is provided. A method of manufacturing a fuel cell, comprising a preparation step of preparing a fuel cell comprising a stack of a plurality of unit cells, each including polymer electrolyte and a catalyst layer, and a removal step of removing organic matter from the fuel cell, is provided. This removal step comprises: a first step of maintaining a voltage of the fuel cell at 0 V so as to desorb organic matter from the catalyst layer; a second step of raising a temperature inside the fuel cell so as to evaporate the desorbed organic matter; and a third step of exhausting the evaporated organic matter from the fuel cell.