Bavachinin (BVC), one of the main bioactive prenylated flavonoids derived from Psoralea corylifolia Linn, has a wide variety of pharmacological effects, such as antiangiogenic, antitumor, antiallergic, anti-inflammatory and antibacterial activities, especially as a pan-peroxisome proliferator-activated receptors agonist. A rapid and sensitive method for quantifying BVC in rat plasma was developed and validated through ultra-high-performance liquid chromatography coupled with electrospray-ionization tandem mass spectrometry. Furthermore, a complete metabolic investigation of BVC was performed through ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. In the pharmacokinetic analysis, BVC exhibited rapid oral absorption (T = 0.68 ± 0.21 h), good elimination (T = 2.27 ± 1.63 h) following oral administration and poor absolute bioavailability (5.27%). Moreover, 11 metabolites of BVC in plasma, urine, bile and feces were characterized. The main metabolic pathways of BVC involved isomeriszation, glucuronidation, sulfonation, hydroxylation, methoxylation and reduction. In conclusion, the present study provides a sensitive quantitative method with a lower limit of quantification of 1 ng/mL and an improved comprehension of the physiological disposition of BVC.