This study explored the glucosinolate (GSL) content in Brassica plants and utilized in silico analysis approach to assess their antioxidant capabilities. GSLs, present abundantly in Brassica vegetables, offer potential health advantages, including antioxidant effects. Employing Ultra-Performance Liquid Chromatography (UPLC) coupled with tandem mass spectrometry (MS/MS), major GSLs were identified in 89 accessions from diverse species and subspecies. Statistical analysis and principal component analysis unveiled significant GSL variation and potential correlations among the Brassica germplasms. This study unveils the dominance of aliphatic GSLs over aromatic and indolyl compounds in all the accessions. Notably, Gluconapin (GNA) (33,049.23 µmol·kg−1 DW), Glucobrassicanapin (GBN) (9803.82 µmol·kg−1 DW), Progoitrin (PRO) (12,780.48 µmol·kg−1 DW) and Sinigrin (SIN) (14,872.93 µmol·kg−1 DW) were the most abundant compounds across the analyzed accessions. Moreover, in silico docking studies predicted promising antioxidant activity by evaluating the interactions of each GSL with antioxidant enzymes. Specifically, Sinigrin and Gluconapin exhibited a notably weaker influence on antioxidant enzymes. This provides key insights into the antioxidant potential of Brassica germplasm and highlights the importance of in silico analysis for evaluating bioactive properties. In general, the results of this study could be utilized in breeding programs to maximize GSL levels and antioxidant properties in Brassica crops and for developing functional foods with enhanced health benefits.