A method for preparing fatty acid alkyl ester for bio-diesels is disclosed, wherein fatty acid, specifically fatty acid distillate reacts with alcohol in the presence of metal catalyst instead of conventional acid or solid acid catalyst. The method does not require the glycerin purification process, and has the superior conversion ratio of fatty acid. The method for preparing fatty acid alkyl ester comprises the step of carrying out an esterification reaction of fatty acid raw material with alcohol in the presence of metal catalyst. Preferably, the esterification reaction is carried out at the temperature of 200 to 350° C. and the pressure of atmospheric pressure to 10 bar, and the metal catalyst is a compound containing metal selected from the group consisting of cobalt, iron, manganese, zinc, titanium and mixture thereof.