Nowadays, the use of the growth regulator salicylic acid for improving a plant’s resistance to environmental stresses such as drought is increasing. The present study investigated the effect of salicylic acid on the physiological traits, antioxidant enzymes, yield, and quality of Allium hirtifolium (shallots) under drought conditions for three years (2016–2017, 2017–2018, and 2018–2019). The experiment was conducted as a split-plot based on a randomized complete block design with four repeats. Irrigation as the main factor in four levels of 100% (full irrigation), 75% and 50% of the plant water requirements with non-irrigation (dryland), and salicylic acid as the sub-factor in four levels of 0, 0.75, and 1 mmol, were the studied factors in this research. The combined analysis of three-year data showed that drought reduced leaf relative water content (RWC), membrane stability index (MSI), chlorophyll content, onion yield, and increased activity of antioxidant enzymes, proline content, tang, and allicin of shallots. Shallot spraying with salicylic acid improved leaf RWC, MSI, chlorophyll content, and onion yield. The highest yield of onion (1427 gr m−2) belonged to full irrigation and foliar application of 1 mmol salicylic acid. The lowest yield (419.8 gr m−2) belonged to plats with non-irrigation and non-application of salicylic acid. By improving the effective physiological traits in resistance to water deficit, salicylic acid adjusted the effects of water deficit on the yield of shallots. Foliar application of 1 mmol salicylic acid in dryland and irrigation of 50% of the plant water requirement increased onion yield by 15.12% and 29.39%, respectively, compared to the control treatment without salicylic acid.