Here, we report for the first time, green-synthesized selenium nanoparticles (SeNPs) using pharmacologically potent herb of Polygonum bistorta Linn. for multiple biomedical applications. In the study, a facile and an eco-friendly approach is utilized for synthesis of SeNPs using an aqueous roots extract of P. bistorta Linn. followed by extensive characterization via Fourier transform infrared spectroscopy, X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and Energy Dispersive X-Ray (EDX) analysis. The XRD and FTIR data determine the phase composition and successful capping of plant extract onto the surface of NPs while SEM and TEM micrographic examination reveals the elliptical and spherical morphology of the particles with a mean size of 69 ± 23nm. After comprehensive characterization, the NPs are investigated for antifungal, antibacterial, antileishmanial, antioxidant, and biocompatibility properties. The study reveals that Polygonum bistorta Linn. synthesized SeNPs exhibit significant antibacterial and antifungal activities with Staphylococcus aureus and Fusarium oxysporum inducing the highest zone of inhibition of 14 ± 1.0mm and 20 ± 1.2mm, respectively at the concentration of 40mg/mL. The NPs are also found to have antiparasitic potential against promastigote and amastigote forms of Leishmania tropica. Furthermore, the NPs are discovered to have excellent potential in neutralizing harmful free radicals thus exhibiting considerable antioxidant potential. Most importantly, Polygonum bistorta Linn. synthesized SeNPs showed substantial compatibility against blood cells in vitro studies, which signifies the nontoxic nature of the NPs. The study thus concludes that medicinally important Polygonum bistorta Linn. roots can be utilized as an eco-friendly, sustainable, and green source for the synthesis of pharmacologically potent selenium nanoparticles.