Fungal endophytes are an essential component of plant ecosystems, residing within plant tissues without causing disease and providing numerous benefits, including enhanced nutrient acquisition, stress tolerance, and pathogen resistance. These fungi exhibit significant diversity, shaped by host specificity, environmental conditions, and climate change. Host identity influences fungal colonization through plant defense mechanisms, nutrient availability, and signaling molecules, while environmental factors such as temperature, soil composition, and moisture levels further regulate endophyte diversity and function. Climate change is emerging as a major driver of shifts in fungal endophytic communities, altering species distribution, symbiotic relationships, and ecosystem stability. Environmental changes on a global scale are causing shifts in the species distributions, consequently altering the interactions between the organisms within ecosystems. These ecosystems comprise a complex web of species with diverse life history strategies and varying dispersal capabilities. It is therefore improbable that all species will respond identically to climatic change. While disruptions in plant interactions have been documented, the impact on plant–endophytic fungi relationships remains understudied. Given the crucial role of endophytic fungi in nutrient cycling, plant nutrition, and facilitation of plant coexistence, as well as population regulation, alterations in these interactions could have significant consequences for plant community composition and overall ecosystem function. Researchers are investigating these endophytic fungi across diverse plant hosts, including forest trees, medicinal plants, and marine organisms, encompassing various ecosystems like terrestrial, freshwater, and aquatic environments. This study focuses on the direct and indirect effects of climate change on endophytic fungi and their interactions with host plants. We identify emerging research questions and areas for future exploration, while also evaluating the potential ramifications of these changing interactions on ecosystem composition and function.