The melatonin molecule is well-known for its benefits to human health. It also mediates many physiological processes in plants. In the current study, the effects of melatonin on the health index and drought tolerance of tomato seedlings have been investigated. Under drought stress, chlorophyll contents and net rates of photosynthesis in tomato seedlings were significantly decreased. As the stress was prolonged, the kinetics of chlorophyll fluorescence was also significantly altered. However, plants pretreated with melatonin (0.1 mM) significantly alleviated these negative outcomes caused by the drought stress and enabled plants to maintain their photosynthetic capacity. The results show that application of melatonin to tomato plants enhances their root vigor, mitigates their stress-related damage to PSII reaction centers, minimizes the negative impact of drought by regulating the antioxidant system and reduces the cellular content of toxic substances of the plants. Current study provides valuable information for growers and breeders to use this approach to produce stronger and drought-tolerant tomato seedlings.