Vegetable oil consumption is expected to reach almost 200 billion kilograms by 2030 in the world and almost 2.97 million tons in Pakistan. A large quantity of edible oil is imported annually from other countries to fill the gap between local production and consumption. Compared to other edible oil crops such as soybean, rapeseed, peanut and olive, sesame has innately higher (55%) oil content, which makes it an excellent candidate to be considered to meet local edible oil production. Oil seed crops, especially sesame, are affected by various pathogens, which results in decreased oil production with low quality oil. Selenium nanoparticles (SeNPs) work synergistically, as it has antifungal activity along with improving plant growth. Different concentrations of SeNPs were used, on three different varieties of sesame (TS-5, TH-6, and Till-18). Plant growth and development were accelerated by SeNPs, which ultimately led to an increase in crop yield. Morphological parameters revealed that SeNPs resulted in a growth increase of 55.7% in root length, 48% increase in leaf number/plant, and 38% in stem diameter. Out of three sesame varieties, TS-5 seedlings treated with 40 mg/L SeNPs showed 96.7% germination and 53% SVI at 40 mg/L. Sesame varieties dramatically increased antioxidant capability using SeNPs, resulting in 147% increase in SOD and 140% increase in POD enzyme units in TH-6 and 76% elevation in CAT enzymes in TS-5 (mean ± S.E). GCMS analysis revealed that bioactive compound I, sesamin, sesamol, and tocopherol contents were increased along with enhanced production of different unsaturated fatty acids. Kegg pathway analysis and MSEA revealed that these compounds were mainly involved in biosynthesis of unsaturated fatty acids, suggesting that SeNPs have elicited the biosynthesis of unsaturated fatty acids such as oleic acid, linoleic acid, and α-linoleic acid. This study concluded that SeNPs (40 mg/L) have an excellent capability to be used for crop improvement along with better oil quality.