The phytotoxicity of chromium (Cr) makes it obligatory for the researchers to develop strategies that seek to hinder its accumulation in food chains. While, protective role of selenium (Se) has not been discussed in detail under adverse conditions in oilseed rape. Here, our aim was to investigate the potential use of Se (0, 5 and 10 μM) in alleviating the Cr toxicity (0, 100 and 200 μM) in Brassica napus L. Results delineated that Se-supplementation notably recovered the Cr-phytotoxicity by reducing the Cr accumulation in plant tissues and boosted the inhibition in plant growth and biomass. Under Cr stress, the exogenously applied Se significantly recovered the impairment in photosynthesis related parameters (chlorophyll a, chlorophyll b, carotenoids, net photosynthetic rate, stomatal conductance, and photochemical efficiency of photosystem II), and counteracted the reduction in nutrients uptake and improved the essential amino acids (EAAs) levels. In addition, Se activated the antioxidants enzymes included in AsA-GSH cycle (SOD, CAT, APX, GR, DHAR, MDHAR, GSH, and AsA) and glyoxalase (Gly) system (Gly I and Gly II) and minimized the excessive generation of reactive oxygen species (ROS) and methylglyoxal (MG) contents in response to Cr stress. In a nutshell, Se (more effective at 5 μM) alleviated the Cr and MG induced phytotoxicity and oxidative damages by minimizing their (Cr and MG) accumulation and enhanced the plant growth, nutrients element level, nutrition quality by improving EAAs, antioxidant and Gly system. By considering the above-mentioned biomarkers, the addition of exogenous Se in Cr polluted soils might be effective approach to decrease the Cr uptake and its linked phytotoxicity in B. napus.