The main aim of the present study was to examine the role of selenium (Se) in ameliorating the toxic effect of cadmium (Cd) in mustard (Brassica juncea) plants. The plants exposed to elevated levels of Cd exhibited reduced biomass, pigment content, and relative water content (RWC). However, supplementation of Se restores the negative effect of Cd and increases biomass, pigment content, and RWC. Osmolyte (proline and glycine betaine) and sugar content were increased under Cd stress and further increase was observed with addition of Se. Cd decreased protein content and supplementation of Se increases it to appreciable levels. Cd also increased production of H2O2 and lipid peroxidation, electrolyte leakage, and the activities of antioxidant enzymes such as superoxide dismutase, ascorbate peroxidase, and glutathione reductase. Supplementation of Se decreased accumulation of H2O2 and lipid peroxidation, increased the activities of antioxidant enzymes to greater levels, and regulates Cd accumulation in roots and shoots. Ascorbic acid (AsA) and flavonoids decreased with elevated concentrations of Cd; however, tocopherol and total phenols were increased with the same concentrations of Cd. Se application maintains AsA and flavonoid content, and further increase in tocopherol and total phenols were observed with Se in the present study. Overall the results confirm that exogenous application of Se mitigates the negative effects of Cd stress in mustard plants through the regulation of osmoprotectants, antioxidant enzymes, and secondary metabolites.