ABSTRACTMelatonin, a multifunctional, non‐toxic regulatory molecule, plays a crucial role in enhancing tolerance to abiotic stress, which is tightly linked to S metabolism. Despite the proven efficacy of sulfur (S) in enhancing abiotic stress tolerance, the combined effect of S and melatonin in stress mitigation remains to be elucidated. This is particularly relevant in the context of climate change, where the increased occurrence of waterlogging stress increases the risk of reduced S availability, leading to reduced yield and quality in rapeseed. The objective of this study is to examine the impact of a combination of foliar melatonin and sulfur, when administered to soil or leaves, on the response of plants to waterlogging stress. The experimental design involved the supplementation of rapeseed (Brassica napus L.) plants with sulfur (S) to either the soil (0.2 g kg−1) or the leaves (300 ppm) 5 days prior to stress induction. The plants were subjected to waterlogging at BBCH–31 for a period of 7 days, preceded by a pretreatment 2 days prior to the stress with melatonin (200 μM). In comparison, untreated plants subjected to waterlogging showed a significant reduction in growth, nutrient uptake, photosynthetic activity, and sugar content but an increase in the antioxidant defense system. However, the application of melatonin significantly mitigated the adverse effects of waterlogging stress. In comparison with the control, soil‐S application exhibited higher efficacy than foliar S application in increasing plant resistance, as reflected by improved dry weight (+50%), photosynthesis (+12%), stomatal conductance (+40%), sulfur (+40%), magnesium (+59%), and reduced hydrogen peroxide (−22%) and lipid peroxidase (−26%). This combination also increased antioxidant defense by increasing catalase (+43%), glutathione reductase (+17%), ascorbate peroxidase (+47%), ascorbate (+39%), and glutathione (+40%) contents, in contrast to untreated waterlogged plants. The study underlines the potential of melatonin and sulfur as effective agents to alleviate waterlogging stress.