Selaginella doederleinii Hieron is a widely used as folk Chinese medicine for treatment of different cancers. Our previous investigations have confirmed that the total biflavonoids in ethyl acetate extract from S. doederleinii (SDEA) have favorable anticancer potentials. However, the in vivo process of its bioactive ingredients remains unknown. In this paper, a sensitive and reliable method was developed for simultaneous quantification of main five biflavonoids, including amentoflavone, robustaflavone, 2″,3″-dihydro-3′,3″-biapigenin, 3′,3″-binaringenin and delicaflavone in the ethyl acetate extract of S. doederleinii (SDEA extract) in rat plasma by high-performance liquid chromatography with electrospray ionization-mass spectrometry (HPLC-ESI–MS/MS). Chromatographic separation was performed using an Ultimate® XB-C18 (100 × 2.1 mm, 3.5 μm) with gradient elution of water (0.5% acetic acid) and acetonitrile at 0.2 mL/min. All analytes with internal standard (chrysin) were detected using selective reaction monitoring (SRM) in negative ionization mode. The method showed a good linearity over a wide concentration range (r2 > 0.99). The limits of quantification for the biflavonoids were less than 10 ng/mL. The developed method was applied to the comparatively pharmacokinetic study of the five biflavonoids after oral or intravenous administration of SDEA extract in rats. In addition, in silico assessments of permeability and solubility of these biflavonoids were also performed to understand their poor bioavailability. It is the first time to report the in vivo process profiles of the biflavonoids of SDEA extract in rats.