Aim Oxidative stress is a key contributor to endothelial dysfunction and associated cardiovascular pathogenesis. Hydrogen sulfide (H2S) is an anti-oxidant gasotransmiter that protects endothelial cells against oxidative stress. Sirtuin3 (SIRT3), which belongs to silent information regulator 2 (SIR2) family, is an important deacetylase under oxidative stress. H2S was able to regulate the activity of several sirtuins. The present study aims to investigate the role of SIRT3 in the antioxidant effect of H2S in endothelial cells. Results Cultured EA.hy926 endothelial cells were exposed to hydrogen peroxide (H2O2) as a model of oxidative stress-induced cell injury. GYY4137, a slow-releasing H2S donor, improved cell viability, reduced oxidative stress and apoptosis, and improved mitochondrial function following H2O2 treatment. H2S reversed the H2O2-mediated inhibition of MAPKs phosphorylation, down-regulated SIRT3 mRNA and enhanced expression of superoxide dismutase 2 and isocitrate dehydrogenase 2. H2S also increased activator protein-1 (AP-1) binding activity with SIRT3 promoter and this effect was absent in the presence of the specific AP-1 inhibitor SR11302 or curcumin. Paraquat administration to mice induced a defected endothelium-dependent aortic vasodilatation and increased oxidative stress in both mouse aorta and small mesenteric artery, which were alleviated by GYY4137 treatment. This vaso-protective effect of H2S was absent in SIRT3 knockout mice. Innovation The present results highlight a novel role for SIRT3 in the protective effect of H2S against oxidant damage in endothelium both in vitro and in vivo. Conclusion H2S enhances AP-1 binding activity with the SIRT3 promoter, thereby up-regulating SIRT3 expression and ultimately reducing oxidant-provoked vascular endothelial dysfunction.