As a major active stilbene from the leaves of pigeon pea (Cajanus cajan), cajaninstilbene acid (CSA) exerts various pharmacological activities. The present study aimed to investigate the pharmacokinetics of CSA and one of its main metabolites (M1) to explore their fate in the body and provide a pharmacokinetic foundation for their in vivo biological activities and functional food or complementary medicine application. M1 was characterized as CSA-3-O-glucuronide using the multiple reaction monitoring-information-dependent acquisition-enhanced product ion technique. After oral and intravenous administration, plasma, urine, and bile were collected and analyzed to estimate pharmacokinetic properties of CSA and M1 and to explore the main excretion route. The oral bioavailability of CSA was estimated to be 44.36%. This study first reported that CSA is mainly metabolized to CSA-3-O-glucuronide via the first-pass effect to limit its oral bioavailability and excreted predominantly through the biliary route, while the enterohepatic circulation, extravascular distribution, and renal reabsorption characteristics of CSA might delay its elimination.