A rapid, selective and sensitive ultra-performance liquid chromatography method with tandem mass spectrometric detection (UPLC–MS–MS) for simultaneous determination of harpagoside and cinnamic acid in rat plasma was developed and validated. The plasma sample preparation was a simple deproteinization by the addition of methanol. Hesperidin was used as the internal standard. The separation was carried out on an ACQUITY UPLC BEH C18 column with acetonitrile and 5 mmol ammonium acetate (35:65, v/v) as mobile phase. The detection was performed by means of electrospray ionization mass spectrometry in negative ion mode with multiple reaction monitoring. The method was validated over the concentration range of 8.00–960 ng mL−1 for harpagoside and 9.90–992 ng mL−1 for cinnamic acid. The intra- and inter-day precisions (relative standard deviations) were within 9.3% and the assay accuracies (relative errors) were −4.2 to 4.6% for harpagoside and 2.6–6.5% for cinnamic acid, respectively. The validated method was successfully applied to the pharmacokinetic study of harpagoside and cinnamic acid in rats after oral administration of Yanyan tablets, a Chinese Traditional Compound Medicine.