Prenylated polyphenols have attracted a lot of interest because of their significant pharmacological activities. The chemoenzymatic synthesis of prenylated polyphenols using prenyltransferase (PT) has been regarded as a promising alternative to chemical synthesis or plant-based production. Psoralea corylifolia L. with abundance of diversified prenylated polyphenol compounds is an ideal material for the discovery of prenyltransferases available in synthetic biology. In this study, we investigated the transcriptomic data from P. corylifolia for prenyltransferases (PcPTs) involved in the biosynthesis of prenylated phenols. Among 11 PcPTs, our yeast expression in vitro survey showed that PcPT11 was able to utilize 23 substrates, including 22 flavonoids and 1 coumarin, and was the one able to use the most substrates. PcPT11 acts in a highly regio-specific way to prenylate flavonoids at the C-6 position to produce compounds with important pharmacological effects such as corylifolinin, wighteone, and bavachin, which are the major ingredients in P. corylifolia. Finally, PcPT11 exhibited strong expression in fruits and leaves, and a GFP-PcPT11 fusion protein was shown to be localized in chloroplasts when expressed in Nicotiana benthamiana. Our study laid a foundation for understanding the biosynthetic pathway of prenylated flavonoids in P. corylifolia, and demonstrated that PcPT11 is a valuable enzyme to produce these pharmaceutically important prenylated polyphenols through biosynthetic approaches.