Selenium (Se) is a microelement that plays an important nutrient role by influencing various physiological and biochemical traits in plants. It has been shown to stimulate plant metabolism, enhancing secondary metabolites and lowering abiotic and biotic stress in plants. Globally, the enormous applications of nanotechnology in the food and agricultural sectors have vastly expanded. Nanoselenium is more active than bulk materials, and various routes of synthesis of Se nanoparticles (Se-NPs) have been reported in which green synthesis using plants is more attractive due to a reduction in ecological issues and an increase in biological activities. The Se-NP-based biofortification is more significant because it increases plant stress tolerance and positively impacts their metabolism. Se-NPs can enhance plant resistance to various oxidative stresses, promote growth, enhance soil nutrient status, enhance plant antioxidant levels, and participate in the transpiration process. Additionally, they use a readily available, biodegradable reducing agent and are ecologically friendly. This review concentrates on notable information on the different modes of Se-NPs’ synthesis and characterization, their applications in plant growth, yield, and stress tolerance, and their influence on the metabolic process.