<p>Oilseed Brassicas, especially <i>Brassica juncea</i>, are valued for their oil content and health-promoting bioactive compounds (tocopherols and phytosterols), while its suitability for human consumption or industrial use depends on its fatty acid composition. Improvement of these traits is a key to enhance the value of this crop, but the genetic basis of these bioactive compounds in <i>B. juncea</i> remains unexplored. The present study aims to identify genomic regions associated with these bioactive compounds in <i>B. juncea</i>. This study examined the oil content, fatty acid composition, and bioactive compounds (tocopherols and phytosterol) in 191 <i>B. juncea</i> accessions over two consecutive years. Genome-Wide Association Study (GWAS) was performed to identify associations between SNPs and seed quality traits. Significant variation was observed for all the studied traits. Thirteen accessions were identified with superior quality traits for potential use in Brassica improvement programs. There was a positive association between eicosenoic and erucic acid, contributing collectively to the very long chain fatty acid (VLCFA) content in the seed oil of this crop. The genomic regions surrounding significant SNPs revealed several functional candidate genes involved in lipid synthesis, tocopherol synthesis, and fatty acid transport. Predicted gene <i>DHS2</i> (<i>3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE 2</i>) appeared important in the inheritance of tocopherols, while two genes, <i>GPS1</i> (<i>GERANYL DIPHOSPHATE SYNTHASE 1</i>) and <i>CPI1</i> (<i>CYCLOPROPYL ISOMERASE 1</i>), were involved in phytosterol formation. The development of high-yielding strains coupled with improved oil quality, enriched tocopherol and phytosterol content has the potential to elevate the value of this crop, accelerating genetic progress via marker-based breeding.</p>