The presented work describes the development and validation of a rapid UHPLC-UV method using a fused core particle column with an RP-Amide stationary phase for the separation and quantitative analysis of caffeoylquinic and di-caffeoylquinic acids in green coffee extracts. Three caffeoylquinic acids (3-caffeoylquinic acid, 4-caffeoylquinic acid, and 5-caffeoylquinic acid) and two di-caffeoylquinic acids (1,3-di-caffeoylquinic acid, and 3,5-di-caffeoylquinic acid) were separated and analyzed in 8 min. That was possible due to the unique selectivity of the RP-Amide stationary phase for the analyzed acids. The retention behavior of all analytes under different compositions of the mobile phase on different columns was evaluated in this study. The optimal chromatographic separation was performed using an Ascentis Express RP-Amide (100 × 2.1 mm) fused-core column with a particle size of 2.7 μm at a temperature of 30 °C. For validation of the newly developed method, acetonitrile was used as mobile phase B and 5% formic acid, filtrated through a 0.22 μm filter, was used as mobile phase A. They were delivered at a flow rate of 0.9 mL min−1 according to the elution gradient program. The detection wavelength was set at 325 nm. A solid-liquid extraction with a solution of methanol and a 5% water solution of formic acid (25 + 75 v/v) using an ultrasonic bath was chosen for the preparation of the available commercial samples of food supplements containing a green coffee extract. Recoveries for all analyzed acids were 98.2–101.0% and the relative standard deviation ranged from 0.3% to 1.4% for intra-day and from 0.3% to 3.0% for inter-day repeatability. The limits of detection were in the range of 0.30–0.53 μg mL−1.