Provided are a method of preparing a fuel cell and a membrane electrode assembly prepared by the method. The method includes preparing a substrate, forming a buffer layer having a single crystalline structure on the substrate, forming a proton conducting solid perovskite electrolyte membrane on the buffer layer, forming a first electrode on one surface of the proton conducting solid perovskite electrolyte membrane, etching the substrate, and forming a second electrode on the opposite surface of the one surface of the electrolyte membrane. Thus, the method of preparing a fuel cell can improve ion conductivity of an electrolyte membrane at a low temperature and a membrane electrode assembly of a fuel cell prepared by the method can improve ion conductivity at a low temperature.