Abiotic stress, particularly salinity, has always posed a significant challenge to crop production, especially in dry and semi-arid regions. Fungal endophytes have shown potential in enhancing plant growth and yield under salt stress conditions. In the present research, the hypothesis whether the endophytic fungus Meyerozyma guilliermondii isolated from a salt-tolerant plant, Typha latifolia, can enhance the growth of wheat under salt stress was tested. The fungus was identified as M. guilliermondii isolate RK01 based on DNA sequence analysis. Firstly, the response of both M. guilliermondii and wheat to NaCl stress was examined individually, while in the second phase, the impact of M. guilliermondii in mitigating the effect of NaCl stress on wheat was evaluated. M. guilliermondii produced a significantly small amount of indole-3-acetic acid (IAA) and gibberellic acid (GA), while a notable increase in abscisic acid (ABA), flavonoids, proline, and carbohydrates was witnessed in the fungus under elevated salt stress. A significant decline in photosynthetic pigments, root length, shoot length, root fresh weight, shoot fresh weight, root dry weight, shoot dry weight, and GA contents was recorded upon exposure of wheat to NaCl stress, while salicylic acid and ABA contents of wheat under the same stress were significantly increased. Upon co-treatment with M. guilliermondii under NaCl stress, all the growth attributes, photosynthetic pigments, and hormones of wheat were significantly improved. Moreover, the combined treatment also resulted in significant reductions in various metabolites, stress markers, free radical scavenging enzymes, and Na+ ion uptake compared to salt stress alone. This study concludes that M. guilliermondii effectively mitigates NaCl stress in wheat and has the potential to alleviate the adverse effects of salinity in other important crops.