The relative standard deviation (RSD) of measurements in high-performance liquid chromatography with electrochemical detection (HPLC-ECD) was predicted by a chemometric tool based on the 1/f fluctuation model which is made up of white noise and a Markov process, called the Function of Mutual Information (FUMI) theory. FUMI theory can provide aprecise and reliable detection limit from a single measurement of noise and signal in HPLC-ECD. To obtain RSD (n = 5) for determination of (-)-epicatechin at five concentrations required 12.5 h, while the predicted RSD by FUMI theory required only 0.5 h (one measurement). Moreover, to trace the source of instrumental noise, power spectra of chromatographic baseline were used. Selection of a suitable apparatus in HPLC-ECD system, acquisition of RSD, and detection limits for determination of catechins by HPLC-ECD were simply and easily made by this chemometric tool within a very short time. The use of the FUMI theory for the prediction of measuring precision was more efficient and the optimization was less time-consuming to be suited for determination.