We investigated the protective role of selenium (Se) in minimizing high temperature-induced damages to rapeseed (Brassica napus L. cv. BINA Sarisha 3) seedlings. Ten-day-old seedlings which had been supplemented with Se (25 μM Na2SeO4) or not were grown separately under control temperature (25 °C) or high temperature (38 °C) for a period of 24 or 48 h in nutrient solution. Heat stress caused decrease in chlorophyll and leaf relative water content (RWC) and increased malondialdehyde (MDA), hydrogen peroxide (H2O2), proline (Pro), and methylglyoxal (MG) contents. Ascorbate (AsA) content decreased at any duration of heat treatment. The content of reduced glutathione (GSH) increased only at 24 h of stress, while glutathione disulfide (GSSG) markedly increased at both duration of heat exposure with associated decrease in GSH/GSSG ratio. Upon heat treatment the activities of ascorbate peroxidase (APX), glutathione S-transferase (GST) and glyoxalase I (Gly I) were increased, while the activities of monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), and catalase (CAT) were decreased. The activities of glutathione reductase (GR) and glutathione peroxidase (GPX) remained unchanged under heat stress. However, heat-treated seedlings which were supplemented with Se significantly decreased the lipid peroxidation, H2O2, and MG content and enhanced the content of chlorophyll, Pro, RWC, AsA, and GSH as well as the GSH/GSSG ratio. Selenium supplemented heat-treated seedlings also showed enhanced activities of MDHAR, DHAR, GR, GPX, CAT, Gly I, and Gly II as compared to heat-treated seedlings without Se supplementation. This study concludes that exogenous Se application confers heat stress tolerance in rapeseed seedlings by upregulating the antioxidant defense mechanism and methylglyoxal detoxification system.