Chromium (Cr) is among the most widespread toxic trace elements found in agricultural soils resulting from various anthropogenic activities. However, the role of micronutrient-amino acid chelates in reducing Cr toxicity in crop plants has recently been suggested. The present study was conducted to explore the effect of iron (Fe) chelated with lysine (lys) on plant growth, biomass, gaseous exchange attributes, oxidative stress indicators, antioxidant response, and Cr uptake in rapeseed (Brassica napus L.) plants irrigated with different levels of tannery wastewater in soil collected from District Kasur of Pakistan. B. napus seedlings (thirty-day-old) were shifted to pots irrigated with different levels of tannery wastewater. After two weeks, foliar application of Fe–lys (5 mM) was carried out for four successive weeks, and plants were harvested carefully post ten weeks of cultivation in tannery wastewater, under controlled conditions. Toxic levels of Cr in the soil significantly decreased plant height, fresh biomass of roots and leaves, dry biomass of roots and leaves, root length, number of leaves, leaf area, total chlorophyll contents, carotenoid contents, transpiration rate (E), stomatal conductance (g_s), net photosynthesis (P_N), and water use efficiency (WUE). Toxic Cr levels in the soil also increased oxidative stress in the roots and leaves of B. napus plants, which were overcome by the activities of various antioxidant enzymes, such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX). Moreover, increasing levels of Cr in the soil caused a significant increase in the Cr content of the roots and shoots of B. napus plants. The negative effects of Cr toxicity could be overturned by Fe–lys application, significantly increasing plant growth, biomass, chlorophyll content, and gaseous exchange attributes by reducing oxidative stress (H₂O₂, MDA, EL) and enhancing antioxidant enzyme activities. Furthermore, foliar application of Fe–lys reduced the Cr concentration and increased essential micronutrients (Fe contents) in the roots and shoots of B. napus plants. These results shed light on the effectiveness of Fe–lys in improving the growth and up-regulation of antioxidant enzyme activities of B. napus in response to Cr stress. However, further studies at field levels are required to explore the mechanisms of Fe–lys-mediated reduction of the toxicity of not only Cr, but possibly also other heavy metals in plants.