Cell wall-associated receptor kinases (WAKs/WAKLs), are a specialized class of plant receptor kinases essential for signaling during stress conditions. However, there has been no report on the involvement of WAKs/WAKLs in salt tolerance in cotton. In this study, we report the functional characterization of GhWAKL26, whose expression is induced by salt, with its levels increasing over time and with higher salt concentrations. In addition, the fusion protein of GhWAKL26 and GFP was localized to the plasma membrane. In transgenic Arabidopsis, the dry weight, fresh weight, and root length were significantly higher than those of wild-type plants, indicating enhanced salt tolerance. While in GhWAKL26-silenced cotton seedlings, H2O2, O2−, and MDA content were increased, and chlorophyll content was reduced under salt stress, displaying compromised salt tolerance. RNA-seq analysis revealed that the silencing of GhWAKL26 resulted in the down-regulation of expression levels of certain ion transport-related genes under salt stress, concurrently leading to an increased Na+/K+ ratio in cotton seedlings. Overall, our findings indicate that GhWAKL26 enhanced plant resistance to salt stress in cotton by regulating the balance of Na+ and K+ ions.