This paper reports the preparation and characterization of a new chlorogenic acid (CHA) certified reference material (CRM), which is unavailable commercially. CHA is an active ingredient found in many geo-authentic Chinese medicinal materials and developed as an anti-cancer drug. In this work, trace impurities were isolated and identified through various techniques. CHA CRM was quantified with two analytical methods, and their results were in good agreement with each other. The certified value and corresponding expanded uncertainty of CHA CRM reached 99.4% ± 0.2%, which was calculated by multiplying the combined standard uncertainty by the coverage factor (k = 2), at a confidence level of 95%. This CRM can be used to calibrate measurement system, evaluate or validate measurement procedures, assign traceable property values to non-CRMs, and conduct quality control assays.