Melatonin (MT) has been reported to regulate certain plant physiological processes and promote tolerance to different environmental stresses such as salinity. Green bean (Phaseolus vulgaris L. cv. Royal Nel) seedlings were exposed to 200 mM NaCl with or without pre-treatment with 150 μM MT. Salt stress led to a lower chlorophyll content, a reduced photosynthetic activity, increased reactive oxygen species (ROS) contents, and decreased photosystem II (PSII) activity. The application of exogenous MT to green bean seedlings under salt stress improved photosynthetic activity and alleviated the oxidative damages by enhancing the activity of antioxidant enzymes. The expression of catalase (CAT1), glutathione reductase (GR), superoxide dismutase (CuZnSOD1), ascorbate peroxidase (APX), Peroxiredoxin Q (PrxQ), and 2-cysteine peroxiredoxin (2-Cys-Prx) encoding genes was significantly increased under salt stress in green bean seedling compared with the untreated control. However, plants treated with exogenous MT and NaCl had 28.8, 21.1, 26.1, 20, 26.2, and 22.4% higher CuZnSOD, CAT1, APX, GR, PrxQ, and 2-Cys-Prx transcript levels, respectively, compared to NaCl stress alone. Our study revealed the protective mechanisms mediated by exogenous MT application in NaCl stress alleviation and our findings could be used in the management of green bean cultivation in salinity-prone soils.