A method for preparing fatty acid alkyl ester for bio-diesel fuel is disclosed wherein fatty acid, specifically fatty acid distillate reacts with alcohol. 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 for bio-diesel fuel comprises the step of carrying out a counter current type esterification reaction of fatty acid and alcohol in each tray of a counter current column reactor at a temperature of 200 to 350° C. and a pressure of 1 to 35 bar. Here the raw material of the fatty acid is fed to an upper part of the counter current column reactor and the alcohol is fed to a lower part of the counter current column reactor. The counter current column reactor has a number of trays which are installed horizontally to have a number of vertical compartments. Each of the number of trays has an opening part at one end thereof to communicate one compartment with an adjoining compartment. The opening parts of two adjoining trays are alternately installed with each other.