The aim of this study was to investigate a validation method for determination of pectolinarin and pectolinarigenin in fermented Cirsium setidens Nakai. For validation, the specificity, linearity, precision, accuracy, detection limits, and quantification limits of pectolinarin and pectolinarigenin were measured by HPLC. The results show that the detection limits of pectolinarin and pectolinarigenin were 4.25 μg/mL and 2.46 μg/mL, respectively. The recovery rates of pectolinarin and pectolinarigenin were high in the ranges of 99.7∼104.0% and 99.7∼102.4%, respectively. Inter-day and intra-day precisions of pectolinarin and pectolinarigenin in fermented Cirsium setidens Nakai were 0.9%, 0.5% and 0.5%, 0.2%, respectively. Therefore, application of pectolinarin and pectolinarigenin was validated by an analytical method as a marker compound in Cirsium setidens Nakai.