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Abstract Drought stress (DS) adversely affects a plant’s development and growth by negatively altering the plant’s physio-biochemical functions. Previous investigations have illustrated that seed priming with growth regulators is an accessible, affordable, and effective practice to elevate a plant’s tolerance to drought stress. Melatonin (MT) is derived from the precursor tryptophan and can improve germination, biomass, and photosynthesis under stress conditions. The current study examined the effect of melatonin seed priming on two wheat cultivars (Fakhar-e-Bhakkar and Akber-19) cultivated under severe drought conditions (35% FC). There were 6 levels of melatonin (i.e., M0 = control, M1 = 1 mg L− 1, M2 = 2 mg L− 1, M3 = 3 mg L− 1, M4 = 4 mg L− 1 and M5 = mg L− 1) which were used for seed priming. Our results confirmed that seed priming with M2 = 2 mgL− 1 concentration of MT alleviates the negative effects of DS by boosting the germination rate by 54.84% in Akber-19 and 33.33% in Fakhar-e-Bhakkar. Similarly, leaf-relative water contents were enhanced by 22.38% and 13.28% in Akber-19 and Fakhar-e-Bhakkar, respectively. Melatonin pre-treatment with 2 mgL− 1 significantly enhanced fresh and dry biomass of shoot and root, leaf area, photosynthetic pigments, osmoprotectants accumulation [total soluble proteins (TSP), total free amino acids (TFAA), proline, soluble sugars, glycine betaine (GB)] and lowered the amount of malondialdehyde (MDA) and hydrogen peroxide (H2O2) production by elevating antioxidants [Ascorbic acid, catalase (CAT), Phenolics, peroxidase (POD) and superoxide dismutase (SOD)] activity under drought stress (DS). Meanwhile, under control conditions (NoDS), the melatonin treatment M1 = 1 mgL− 1 effectively enhanced all the growth-related physio-biochemical attributes in both wheat cultivars. In the future, more investigations are suggested on different crops under variable agroclimatic conditions to declare 2 mgL− 1 melatonin as an efficacious amendment to alleviate drought stress.