Due to the adverse impacts of climate change, diminishing agricultural land, and limited water resources, there is continuous pressure on researchers to improve agricultural productivity for the increasing population. Endophytic fungi (EF), a diverse group of microbes that colonize plant tissues without causing damage, have gained considerable attention due to their positive role in agriculture. This chapter explores the important phytohormones produced by EF, for instance, gibberellic acid (GA), indole-3-acetic acid (IAA), and abscisic acid (ABA), and their key roles in agronomy. IAA and GA production by EF is associated with enhanced plant growth, water uptake, and nutrient availability. Additionally, ABA production alleviates stress conditions such as nutrient deficiency, allowing plants to survive severe drought and salinity for short periods while also influencing secondary metabolites production such as flavonoids, phenols, terpenoids, and steroids. Despite these positive outcomes, the practical application of EF in agriculture is hindered by various factors such as large-scale inoculum production, regulatory standards, and field validation. This chapter highlights the diversity of EF, investigating their abundance and the rationale behind host plant selection. A major focus is to elaborate on the biosynthetic pathways for phytohormone production by EF, with insight into IAA and its multiple biosynthetic pathways. The pathway for GA production is also discussed. This chapter debates the role of essential factors in agriculture and highlights their potential applications in improving plant growth and stress tolerance.