Selenium (Se) deficiency is believed to be involved in pathogenesis of Alzheimer's disease (AD) due to failure of antioxidant system. Its supplementation may restore the antioxidant system and compensate the impairments caused by AD. Present study reveals the effect of Se on the proteomic changes in cortex within triple transgenic male AD mice (3 × Tg-AD) after 4 months sodium selenate supplementation. Using iTRAQ comparative proteomics approach, 142 proteins found significant alterations with 96 down-regulated and 46 up-regulated proteins in the cortices of AD mice in comparison with the wild non-transgenic type mice. On treatment with sodium selenate, 41 proteins showed reverse expression, that is, thirty three proteins were down-regulated in AD mice but up-regulated in selenate treated AD mice while eight up-regulated proteins in AD mice showed lower expression in selenate treated mice. OmicsBean bioinformatics analysis revealed that Se positively affected the proteins vital in biological process, structural cores, and molecular functions, which include metabolic proteins, structural proteins, signaling molecules, oxidative stress balancers, and proteosomal degradation proteins. Results of mass spectrometry (MS) were further confirmed by Western blot analysis of five important proteins, prompting the authenticity of the MS results. This paper fills the protein-based molecular gap between AD and Se-treatment, and it provides a full view of Se in reversing the change of cortical protein levels during AD formation.