Yongdamsagan-tang has been used to treat the urinary disorders, acute- and chronic-urethritis, and cystitis in Korea. In this study, an ultra-performance liquid chromatography-electrospray ionization-mass spectrometry (UPLC-ESI-MS/MS) method was established for simultaneous analysis of the 20 bioactive marker compounds, geniposidic acid, chlorogenic acid, geniposide, liquiritin apioside, acteoside, calceolarioside B, liquiritin, nodakenin, baicalin, liquiritigenin, wogonoside, baicalein, glycyrrhizin, wogonin, glycyrrhizin, wogonin, saikosaponin A, decursin, decursinol angelate, alisol B, alisol B acetate, and pachymic acid in traditional herbal formula, Yongdamsagan-tang. Chromatographic separations of all marker compounds were conducted using a Waters Acquity UPLC BEH C18 analytical column (2.1 × 100 mm, 1.7 μm) at 45°C using a mobile phase of 0.1% (v/v) formic acid in water and acetonitrile with gradient elution. The MS analysis was performed using a Waters ACQUITY TQD LC-MS/MS coupled with an electrospray ionization source in the positive and negative modes. The flow rate was 0.3 mL/min and injection volume was 2.0 μL. The correlation coefficient of 20 marker compounds in the test ranges was 0.9943-1.0000. The limits of detection and quantification values of the all marker components were 0.11-6.66 and 0.34-19.99 ng/mL, respectively. As a result of the analysis using the optimized LC-ESI-MS/MS method, three compounds, geniposidic acid (from Plantaginis Semen), alisol B (from Alismatis Rhizoma), and pachymic acid (from Poria Sclerotium), were not detected in this sample. While the amounts of the 17 compounds except for the geniposidic acid, alisol B, and pachymic acid were 0.04-548.13 μg/g in Yongdamsagan-tang sample. Among these compounds, baicalin, bioactive marker compound of Scutellariae Radix, was detected at the highest amount as a 548.13 μg/g.