An electrochemical method was developed for biodiesel, i.e., fatty acid methyl ester (FAME), production. A two-compartment cell completed with a cation-exchange separating membrane was utilized to minimize recombination between protons and hydroxide or methoxide ions, which leads to the low product yield. In addition to the product yield increase, the method was found to reduce the requirement of organic salt to be only in the cathode chamber. Electrolysis at low voltage (4.6 V) resulting high product yield (ca. 94% in 2 h) at Pt as well as a boron-doped diamond (BDD) electrode as the cathode, suggested the system was free from the dependence on electrode types.