Gypenoside LVI, one of the major bioactive triterpene saponins in Gynostemma pentaphyllum, has been regarded as a potential and promising lead drug for anti-tumor strategy. To better understand the pharmacological activities of the component, an investigation of its in vivo metabolism is important and necessary. In the present study, a liquid chromatography-ion trap time of flight tandem mass spectrometry has been utilized to discover and identify the metabolites of gypenoside LVI in rat urine after oral and intravenous administration. Negative electrospray ionisation mass spectrometry was used to discern gypenoside LVI and its possible metabolites in urine samples. As a result, after oral and intravenous administration, eight and six metabolites together with gypenoside LVI were detected and identified in rat urine, respectively. As metabolites of gypenoside LVI, they have never been reported before. Deglycosylation and dehydration were found to be the major metabolic processes of gypenoside LVI in rat.