• NaCl inhibited the growth and increased Na and Cl concentrations in rice leaves. • Application of Fe mitigated adverse effects of NaCl on rice growth. • Fe-supply enahnced plant antioxidant enzymatic activity in rice plants. • Fe-supply improved CEC of the soil and limited Na uptake by rice. Soil salinity affects plant growth and results in decreased agriculture productivity throughout the world. The present study was carried out to elucidate underlying mechanisms responsible for soil salinity tolerance in rice under the application of iron (Fe) as Fe(NH 4 ) 2 (SO 4 ) 2 ·6H 2 O. Rice seedlings were grown in pots containing soils (pH >8.0) and exposed to 0 and 150 mM (EC of 5.25 dS m −1 ) NaCl stress both with and without 0.5 mM Fe(NH 4 ) 2 (SO 4 ) 2 ·6H 2 O. Plant growth attributes like root length, shoot length, roots and shoots biomass, leaf chlorophyll contents, salt ions, plant mineral concentrations, plant antioxidant activities and cation exchange of soil were determined. Application of NaCl at the rate of 150 mM reduced the leaf chlorophyll contents (34%), root fresh and dry weights (39% and 45%), shoot fresh and dry weights (35% and 53%), grain yield (39%), potassium (K) (59% and 48%), calcium (Ca) (39% and 24%), and magnesium (Mg) (59% and 50%) concentrations in roots and leaves, whereas enhanced the sodium (Na) (537% and 500%) and chloride (Cl) (425% and 156%) accumulation both in roots and leaves as compared to control. Interestingly, Fe-supply enhanced the Fe uptake by rice plants and mitigated the adverse effects of salinity on rice growth and yield by 30%. Moreover, plant antioxidant enzymatic activity and cation exchange capacity (CEC) of soil (cmol Na + kg −1 ) were enhanced by Fe-supply. In conclusion, Fe-application enhanced tolerance in rice due to down regulation of Na and up-regulation of Fe and antioxidant enzymatic activity in leaves. In addition, increased Na adsorption onto the surface of soils suggests that Fe competes with Na at soil-root interface, thereby limiting Na uptake by the plants.