Disclosed is a method for preparing fatty acid alkyl ester for bio-diesel fuels by reacting a raw material containing fat with water to prepare fatty acid, and then reacting the prepared fatty acid with alcohol. The method for preparing fatty acid alkyl ester for bio-diesel fuels includes the steps of: preparing fatty acid and glycerin by an hydrolysis reaction of a raw material containing fat and water at the temperature of 200 to 280°C and the pressure of 30 to 80 bar; carrying out a phase separation of the fatty acid and the glycerin; and carrying out an esterification reaction of the separated fatty acid and alcohol at the temperature of 200 to 350°C and the pressure of atmospheric pressure to 35 bar.