Herbal formulations consist of a wide range of chemical constituents; most of the time, the active constituents are not known. Standardization of therapeutically active marker compounds is essential for quality assessment of an herbal formulation. HPLC method is one of the popular methods for standardization of marker compounds. In the current study, a novel, cost-effective RP-HPLC technique was established and validated for the simultaneous estimation of standard samples of Chlorogenic acid and Eugenol, as there were no methods available for their simultaneous estimation. The separation was carried out by using Shiseido Capcell pak C18column (250 x 4.6mm, 5µ) accompanied by mobile phase, Methanol: Acetonitrile: 0.1%formic acid (20:20:60 v/v/v) with rate of flow 1ml/min in isocratic mode. The eluents, Chlorogenic acid and Eugenol were detected at 211nm using UV-Visible detector and were eluted with retention times of 3.335min and 4.306min respectively. The optimized method was validated according to ICHQ2 (R1) guidelines. Linearity was observed from 1-5µg/ml with correlation coefficient of 0.995 for Chlorogenic acid and 0.996 for Eugenol. LOD (0.05µg/ml) and LOQ (0.1µg/ml) were same for Chlorogenic acid and Eugenol and were calculated based on signal to noise ratio. The % recovery of Chlorogenic acid and Eugenol were 99.42 - 100.06 and 99.50 - 100.30 respectively. The developed and validated technique was successfully extended to quantify marker compounds, Chlorogenic acid and Eugenol in Clearstone drops, which is a polyherbal Homeopathic formulation. The resolution and peak symmetry of the marker compounds quantified in the formulation were same as that of standard marker compounds. The developed technique was found to be suitable for simultaneous quantification of standard samples of Chlorogenic acid and Eugenol as well as for their simultaneous determination in the Clear stone formulation.