Background: Stachys schimperi Vatke has been previously reported for its analgesic, antipyretic, antioxidant, antimicrobial and cardioprotective properties. Objectives: Phytochemical analysis and assessment of anti-hepatitis B virus (anti-HBV) activity of S. schimperi. Materials and Methods: Surface extraction was performed to isolate the phytoconstituents using chromatographic techniques, including HPLC. The isolates were identified by a 1D and 2D NMR spectroscopic data. Further, the isolates were tested for cytotoxicity using an MTT assay. Non-cytotoxic doses of the isolates were assessed for their antiviral potential on cultured HepG2.2.15 cells. To rationalize the plausible mechanisms of the tested anti-HBV active compounds, molecular docking studies were carried out using HBV polymerase (Pol) enzyme. Results: The NMR data proved the structure of isolates as artemetin [5-hydroxy, 3' 3′,4′'6,7-penta methoxy flavone] (1), chrysosplenetin [5,4′-dihydroxy, 3'3′' 6,7-tetra methoxy flavone] (2) and calycopterin [5,4′-dihydroxy, 3' 6,7'8-tetra methoxy flavone] (3). Notably, this is the first report on the isolation of these three compounds from S. schimperi as well as artemetin and calycopterin from the genus Stachys. Further antiviral assessment of the non-cytotoxic dose showed marked inhibitions of HBV antigens (HBsAg/HBeAg) by artemetin (52.28%/46.52%) and calycopterin (61.24%/57.26%) in HepG2.2.15 cells. Chrysosplenetin, however, did not show any anti-HBV activity. Artemetin and calycopterin exhibited anti-HBV activity, possibly through inhibition of HBV-Pol as revealed by molecular docking. Conclusion: We report the identification of anti-HBV active flavones artemetin and Calycopterin from S. shimperi. Our data strongly warrant further molecular and pharmacological studies on artemetin and calycopterin toward developing potential anti-HBV therapeutics.