The current study aimed at assessing the potential effects of Se applied at three levels (0, 20, and 40 mM) in two methods (soil addition or foliar spraying) on the physiological attributes in tomato plant growing under irrigation water deficit (from 100% to 60% of soil field capacity; SFC) during the 2017 and 2018 seasons. The results indicated that reducing irrigation water from 100% to 60% of SFC led to a marked increase in electrolyte leakage (EL), which associated with increased contents of osmoprotectants. In contrast, relative water content (RWC), membrane stability index (MSI), photosynthetic efficiency, and Se content were decreased in both seasons. Both 20 and 40 mM Se significantly increased contents of osmoprotectants, which were reflected in reduced EL and photosynthetic efficiency, and Se content. Compared to foliar spray, better results were obtained with Se application to the soil. The interaction among the three factors; water deficit, Se level, and Se application method was significant. The combination of irrigation at 60% of SFC × 40 mM Se application to soil was preferable, which can be recommended for use for tomato to increase its content of osmoprotectants and Se when cultivated in a dry environment.