Eleutheroside B and Eleutheroside E, two kinds of the major bioactive saponins of Eleutherococcus senticosus, play a pivotal role in biologic activity. In this study, a specific and sensitive high performance liquid chromatography–electrospray ionization-tandem mass spectrometry method (HPLC–MS/MS) was developed and validated for simultaneous determination of Eleutheroside B and Eleutheroside E in rat plasma. The analytes were extracted from rat plasma via a simple protein precipitation procedure with methanol and polygonin was used as internal standard. Chromatographic separation was achieved on a C18 column using a gradient elution program with acetonitrile and water containing 0.1% ammonium hydroxide solution as the mobile phase, with a flow rate of 0.2 mL/min. The detection was performed on a triple–quadrupole tandem mass spectrometer by multiple reactions monitoring (MRM) mode in a negative ion mode via electrospray ionization (ESI). The transition monitored were m/z 371 [M−H]− → 209 for Eleutheroside B, m/z 741[M−H]− → 579 for Eleutheroside E and m/z 389[M−H]− → 277 for internal standard. Linear calibration curves were obtained in the concentration range of 1–2000 ng/mL for both (Eleutheroside B and Eleutheroside E), with a lower limit of quantification of 1 ng/mL. Extraction recovery was over 80% in plasma. The intra- and inter-day precision (RSD) values were below 12% and accuracy (RE) was −2.80 to 5.70% at three QC levels for both. The assay was successfully applied to study pharmacokinetics behavior in rats after oral and intravenous administration of the single substances (Eleutheroside B and Eleutheroside E). And further research was performed by comparing the difference in pharmacokinetic behavior between the single substances and an aqueous extract of E. senticosus after oral administration. Significant difference in pharmacokinetic characteristics between the single substances and an aqueous extract was found in rat, which would be beneficial for the pre-clinical research and clinical use of E. senticosus.