Arsenic is a nonessential toxic metalloid hampering the growth and development of plants. The cotton (Gossypium hirsutum) is of great economic importance in the textile industry as well as in the production of edible oil. In developing countries, especially Pakistan, the export of cotton has a distinct position. However, there has been a signifcant decline in cotton production over the past few years due to climate change, heavy metals induction and biotic stresses. A notable decrease in cotton growth and product is observed in response to arsenic stress. Selenium nanoparticles (Se NPS) were prepared by green chemistry approach and characterized by UV–Vis, FTIR, and XRD to mitigate the heavy metals induced toxicity in cotton seedling. Results shows that arsenic toxicity causes a drastic decrease in photosynthesis, phenolics, proteins, growth of seedlings, relative water content, and overall plant biomass. However, these physio-biochemical attributes were upregulated by applications of Se NPs. Moreover, As stress causes severe oxidative damage by overproduction of MDA, H2O2 and reactive oxygen species (ROS). The supplementation of SeNPs positively regulate the As stress in cotton seedlings by altering important antioxidant enzymes involved in ROS detoxifcation such as SOD, POD, and CAT. Se NPs ameliorate the toxicity by increasing activities of enzymatic and non-enzymatic antioxidants. The accumulation of As in roots alter the architecture of roots including reduced branching of roots. Current results suggest that the applications of selenium nanoparticles especially 20 mg/L concentration confdently alleviate the As induced toxicity in cotton seedlings.