An effective method of high performance liquid chromatography-diode array detector (HPLC-DAD) was developed for the simultaneous quantification of two marker compounds, pectolinarin and pectolinarigenin, in Cirsium setidens Nakai, a Korean wild herb. The two marker compounds of C. setidens were separated on a C18 column with a gradient system. The calibration curves of the two standard compounds exhibited good linearity ($R^2$ >0.9992). The limits of detection (LOD) values of pectolinarin and pectolinarigenin were 0.52 and 0.41 ${mu}g/mL$, respectively, while their limits of quantification (LOQ) values were 1.57 and 1.25 ${mu}g/mL$, respectively. The relative standard deviations (RSDs) of the data of the intra- and inter-day experiments were less than 1.65 and 2.78%, respectively. The results of the recovery test were 98.06-105.81% with an RSD value of 1.87-3.50%. In conclusion, the results of validation showed that the proposed HPLC method was useful for the quantification of the two marker compounds in C. setidens.