Chrysotoxine (CTX), a naturally occurring bibenzyl compound isolated from Dendrobium species, has been reported to have neuroprotective effects. To evaluate its pharmacokinetics in rats, a rapid, sensitive and specific high performance liquid chromatography-tandem mass spectrometric (HPLC-MS/MS) method has been developed and validated for the quantification of CTX in rat plasma. Samples were pretreated using a simple liquid-liquid extraction with ethyl acetate and the chromatographic separation was performed on a C18 column with acetonitrile-water (90:10, v/v) as the mobile phase. CTX and the internal standard (wogonin) were detected using a tandem mass spectrometer in positive multiple reaction monitoring mode. Method validation revealed excellent linearity over the range 0.5-1000 ng/mL together with satisfactory intra- and inter-day precision, accuracy and recovery. Stability testing showed that CTX spiked into rat plasma was stable for 8 h at room temperature, for up to two weeks at -20 °C, and during three freeze-thaw cycles. Extracted samples were also observed to be stable over 24 h in an auto-sampler. The method was successfully used to investigate the pharmacokinetic profile of CTX after oral (100 mg/kg) and intravenous (25 mg/kg) administration in rats. CTX showed rapid excretion and low bioavailability in rats.