Provided are a polymer electrolyte membrane that is stable even at high temperatures in non-humidified conditions, thereby having high proton conductivity, a method of preparing the polymer electrolyte membrane described above, by which high productivity can be obtained, and a fuel cell with high power generation characteristics by using the polymer electrolyte membrane. In particular, there is provided a method of preparing a polymer electrolyte membrane in which a mixed solution prepared by dissolving a (hydrocarbon-based) polymer electrolyte having an acidic functional group and any one free acid source selected from the free acid, mixtures of a free acid and Lewis acid, and mixtures of a free acid and an organic salt in a polar organic solvent is subjected to wet membrane formation to prepare a polymer electrolyte membrane in which the polymer electrolyte is doped with the free acid.