The sex-dependent differences in the response to salt stress of the dioecious Rumex thyrsiflorus and the influence of different concentrations of sodium chloride (NaCl) on the biosynthesis of phenolic compounds in callus suspension cultures were evaluated. The cultures originated from callus obtained on hypocotyls isolated from male and female seedlings were cultured on Murashige and Skoog medium supplemented with 0.4 mg/L 6-benzylaminopurine and 1 mg/L 2,4-dichlorophenoxyacetic acid. The results showed that the response to salt stress depends on both the sex of the plant and the NaCl concentration in the culture medium. The analysis of the main morphometric parameters showed that callus tissue derived from the hypocotyls of female seedlings was less sensitive to salt stress than that from male seedlings, which was correlated with higher concentrations of phenolic compounds. The optimal NaCl concentration to increase the production of phenolic compounds was 129 mM for females and 43 mM for males. In the methanolic tissue extracts 22 compounds were determined using the HPLC–DAD method. In general, higher amounts of compounds were detected in the extracts from the female tissue. The following dominated: catechin (max. 213.31), cryptochlorogenic acid (max. 76.35) and epicatechin (max. 54.84) (mg/100 g DW). This comprehensive phytochemical analysis of the sex-related aspects of the response to salt stress was performed for the first time in this dioecious model species. The results revealed potential application of NaCl as the ecological friendly and inexpensive elicitor to increase the production of pharmaceutically valuable compounds and highlight the importance of dioecy in phytochemistry.