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s-allyl glutathione (SAG) an analogue of glutathione is explored for its antioxidative and liver protection property in recent years. Selenium nanoparticles (Sh-SeNPs) were synthesized using medicinal plant Spermacoce hispida and conjugated with SAG (SAG-Sh-SeNPs). SAG-Sh-SeNPs and Sh-SeNPs were characterized using by Fourier transform infrared spectroscopy, Transmission electron microscopy, Energy dispersive X-ray analysis, X-ray diffraction analysis and zeta potential analysis. SAG-Sh-SeNPs and Sh-SeNPs were evaluated against acetaminophen (APAP)-induced liver and kidney injury in rat. Pretreatment of NPs attenuated the APAP toxicity-induced elevation of kidney and liver injury markers in the blood circulation. Histological observation showed that NPs pretreatment protected the morphology of liver and kidney tissue. SAG-Sh-SeNPs showed enhanced protection against APAP toxicity in comparison to Sh-SeNPs due to synergistic effect of SAG and Sh-SeNPs. SAG-Sh-SeNPs protected the liver and kidney against APAP toxicity through reducing oxidative stress, enhancing endogenous antioxidants and protecting mitochondrial functions.