An analytical technique has been developed to detect trace amounts of both (+)-catechin and (−)-epicatechin in the coconut water extract. Both (+)-catechin and (−)-epicatechin in the coconut water were found for the first time by the solid-phase extraction, and they were further analysed using liquid chromatography (LC)–ion trap mass spectrometry (MS) equipped with positive atmospheric pressure chemical ionisation interface on multiple reaction monitoring mode. The limit of detection and quantification for (+)-catechin were 7.8 and 15.6 μg/ml, respectively, while those for (−)-epicatechin were 3.9 and 7.8 μg/ml, respectively. The average concentration of (+)-catechin and (−)-epicatechin in the coconut water was 0.344 and 0.242 μg/ml, respectively. The LC–MS/MS analysis accelerated the quantitative analysis of (+)-catechin and (−)-epicatechin in the coconut water extract with high accuracy, precision and recovery. Results obtained in this study will serve as quality control and useful reference for drug development.