In the present study, we investigated the ameliorative effects of 24-epibrassinosteroid (24-epiBL) on antioxidant response and ion homeostasis in two NaCl-stressed Linum usitatissimum L. (flax) cultivars differing in salt tolerance. The content and profile of amino acids were also studied in the tolerant cultivar. Salt stress differently altered the activity of antioxidant enzymes, phenol and flavonoid contents, total antioxidant capacity and ion homeostasis in both cultivars, whereas H2O2 and malondialdehyde (MDA) contents were induced only in the TN-97-95 cultivar. Free amino acid concentrations showed variable patterns under salinity conditions compared with the control plants. 24-epiBL decreased the soluble protein content in NaCl-treated plants and also decreased stimulatory effects of salinity on the production and accumulation of phenol and flavonoid contents and antioxidant capacity with altered ion (Na+, K+, and Cl-) contents. The 24-epiBL reduced the chlorophylls (a, b) and carotenoid contents in salt-treated TN-97-95 cultivar while enhanced the activity of antioxidant enzymes and declined the H2O2 content and lipid peroxidation in both NaCl-stressed cultivars. The profile and content of amino acids were significantly changed by 24-epiBL application under salinity treatment. In summary, our findings demonstrate that 24-epiBL seed priming mitigates the deleterious effects of salt stress in flax plants.