Pimpinella pruatjan Molk is native to Java and well known as aphrodisiac in traditional medicine. A water-boiled extract of the plant has been used in the treatment of erectile dysfunction (ED). No study has been found on the phytochemical constituents and identification of corresponding biological activities in water and polar extract. This study is aimed to identify phytoconstituents of a decoction and ethanol extract from the aerial parts of P. pruatjan Molk. Liquid chromatography-tandem mass spectroscopy (LC-MS/MS) was used to analyze and predict the bioactive compounds in both extracts. LC-MS/MS revealed both extracts contained two important compounds: Luteolin-7-O-β-D glucopyranoside and Undulatoside A. Luteolin and Luteolin glucoside are also found in P.anisum L. Lutein 7-O glucoside was found in water extract, while more bioactive compounds, including populnin, 3,5-O-dicaffeoylquinic acid, quercetin-3’- O glucoside, methylophiopogononeone-A, kaempferol-7-O-α-L-arabinofuranoside, and 7-hydroxy-3,5,6,3’,4’- pentamethoxyflavone, were found in ethanol extract. Accumulation of flavonoids, phenols, phenylpropanoids, alkaloids, and furanochromone in low quantities was observed in both extracts. This is the first report providing evidence justifying its use as a traditional medicine. Further investigation into the pharmacology mechanism of action is required.