This work was conducted to obtain a rapid, accurate, and precise procedure for free amino acids analysis in Doenjang with HPLC-OPA (high performance liquid chromatography using-phthalaldehyde) and AAA (automatic amino acid analyzer) methods. Different sample extraction procedures among water, 0.1 M perchloric acid, and 0.1% meta-phosphoric acid were also compared. The optimal extraction solvent was 0.1% meta-phosphoric acid for both the HPLC-OPA and AAA methods. Good recoveries for glycine and methionine were observed using the 0.1% meta-phosphoric acid extraction with HPLC-OPA method. Method precisions (% relative standard deviation) for the free amino acids ranged for 1.62% to 8.27%, in which the HPLC-OPA method with water extraction showed the lowest value at 1.62%. Inhibition rates of the free amino acids in Doenjang were greatest with an addition of NaCI at a 1% concentration.