Context: Genistein and daidzein, major isoflavone aglycone compounds contained in tempeh, became an interesting subject since their activities as cancer prevention, cardiovascular, and wound healing agents. It is important to develop an efficient extraction method to obtained genistein and daidzein from tempeh. Aims: To optimize extraction process of the two compounds from dried tempeh. Methods: The full factorial design was used to analyze the effect of combining factors affecting the extraction process. Genistein and daidzein analysis have been performed by using a C18 column of Phenomenex® (250 x 4.6 mm, 5 µm) and a mobile phase containing methanol:distilled water (70:30). The detection was carried out at 261 nm with a flow rate of 0.6 mL/min in the isocratic reverse-phase HPLC system. Results: The analytical method was validated according to AOAC guidelines including the parameters of selectivity, linearity, accuracy, precision, limit of detection, and limit of quantification. Conclusions: The optimal extraction condition was achieved at the ethanol concentration of 96%, the particle size of 0.6 mm and extraction time of 270 minutes. Total amount obtained from the extraction method was 26.03 mg% and 19.42 mg% for genistein and daidzein, respectively.