For the quantitative analysis of phenolic compounds in beverage samples, a three-flow channel isocratic HPLC with electrochemical detection (3LC-ECD) system was devised using a column-switching technique. Phenolic compounds with significantly different hydrophobicity (the range of calculated log P: −0.77 to 3.02) were simultaneously measured to draw three chromatograms by the 3LC-ECD; the peaks of gallic acid (GA), protocatechuic acid (PCA), and gallocatechin (GC) were observed at electrochemical detector 1 (D1) within 42 min, the peaks of procyanidin B3 (B3), epigallocatechin (EGC), catechin (C), epicatechin (EC), procyanidin B2 (B2), ethyl gallate (Eg), and epigallocatechin gallate (EGCg) were observed at D2 within 50 min, and the peaks of epicatechin gallate (ECg), gallocatechin gallate (GCg), catechin gallate (Cg), propyl gallate (Pg), and resveratrol (RVT) were observed at D3 within 70 min. The relationships between the phenolic compound concentrations and their chromatographic peak heights gave good linearity with correlation coefficients of more than 0.998. The detection limits of the phenolic compounds by the 3LC-ECD ranged from 0.6 to 3.0 µg/L. Further, the phenolic compound concentrations of commercially available teas and wines were determined with a relative standard deviation (RSD) of less than 4.9% (n = 6), and their recoveries ranged from 91 to 109%. These results indicate that the 3LC-ECD system provided an accurate, precise, and specific determination of the phenolic compounds in beverages without affecting the matrices derived from these samples.