The purpose of this study is to investigate the changes occured on phenolic compounds between two Malaysian varieties of pummelo fruit juice: Ledang (PO55) and Tambun (PO52) post-enzymatic clarification. The changes in polyphenols composition were monitored using High Performance Liquid Chromatography Diode Array Detection and Folin Ciocalteu's method. Clarification treatment of pummelo fruit juice with a commercial pectinase was optimized based on incubation temperature, time and enzyme concentration. Both varieties of pummelo fruit juice were treated with different optimized variables which produced the highest clarities with the least effect to the juice physical quality. Tambun variety was found to have significantly more total phenolic compounds (p <0.05) in comparison to Ledang variety, possibly due to the amount of naringin. Three types of hydroxycinnamic acids (chlorogenic, caffeic and coumaric acid) and three compounds of flavanones (naringin, hesperidin and narirutin) were found in both fruit juices, where naringin and chlorogenic acid were the major contributor to the total phenolic content. Naringin, which gave out bitter aftertaste to the juice, was found to decrease, 1.6 and 0.59 % reduction in Ledang and Tambun respectively, post-enzymatic treatment. The decrease in naringin, albeit nominal, could be a potential benefit to the juice production in reducing the bitterness of the juice. Post-enzymatic analysis furthermore resulted in no significance differences (p <0.05) on the total phenolic compounds of both varieties. This study in summary provides a compositional database for Malaysian pummelo fruit juice of various phenolic compounds, which can provide useful information for evaluating the authenticity and the health benefits from the juice.