<p>Salinity is considered one of the most significant abiotic stresses for plants because it reduces agricultural yield by more than 20% of the world’s irrigated land. To resolve this issue, developing of salt-tolerant crops is critical, costly, and time-consuming. Deciphering processes that allow plants to flourish in saline environments may be an alternative. This review describes the effectiveness of endophytic fungi used in crops as supplements to host plants. This is performed by activating antioxidant mechanisms to scavenge ROS, boost beneficial metabolite levels, promote systemic resistance, and control phytohormones during plant development. By regulating ion accumulation, fungal endophyte associations enhance nutrient absorption, maintain ionic homeostasis, maintain a minimal cytosolic Na⁺/K⁺ ratio, and restrict Na⁺ transport to leaves. In the presence of fungal endophytes, transcription factors encoding high-affinity potassium transporter 1 (HKT1) and inward rectifying K⁺ channels KAT1 and KAT2 increased. Under salt stress, endophytic fungi colonization in plants enhance photosynthetic and water-use efficiency. At the molecular level, fungal endophytes influence the expression of plant genes involved in proline, aquaporin, and auxin production. Fungal endophytes can colonize host plants and help maintain higher water content in plant tissues under stress conditions. However, only limited evidence exists regarding their potential role in regulating plant genes involved in ion transport, such as those encoding Na⁺/H⁺ antiporters or cyclic nucleotide-gated channels. The participation of these cation-proton exchangers and channels in the endophyte-mediated response to salt stress represents a promising area of research. Investigating these mechanisms may uncover novel pathways by which endophyte colonization enhances plant salt tolerance. Future research should prioritize the genetic, molecular, and biochemical processes that underpin this improved stress resistance.</p>