Salinity reduces the uptake of manganese (Mn) and induces its deficiency, which adversely affects photosynthesis-related photosystem-II activity, hence growth is hampered. The objective of the study was to investigate the effects of Mn application on the photosystem-II activity on the isolated thylakoid membranes of the rice. A hydroponic study was carried out in the glasshouse of National Agriculture Research Centre, Islamabad, Pakistan on two rice varieties, Pakhal and KS-282, using three replicates. Three salt concentrations, namely 0, 25, 50 mM NaCl were used. Manganese sulphate was used for foliar and root application with four concentrations (0, 2, 4, 8 µg Mn mL -1 ). Salinity decreased the concentration of Mn, while the application of Mn, increased the contents of Mn in shoot and root. Increased salt concentration caused a decrease in the chlorophyll contents while Mn application increased chlorophyll contents across all the salinity levels, with maximum increase at 2 µg Mn mL -1 . Photosystem-II activity was inhibited by increasing salt concentration, while Mn treatment rescued this inhibitory affect, with maximum photosystem-II activity recovery at 2 µg Mn mL -1 level in both varieties. Quite high concentration of Mn was observed in root application methods as compared to foliar but it failed to recover salinity impact on photosystem-II and photosynthesis. Applying Mn as foliar increased tolerance to salinity at 50 mM NaCl level while root application was found better at 25 mM NaCl concentration in culture solution.