Fungal endophytes are a diverse group of fungi that live inside plant tissues without causing apparent harm to the host plant. This symbiotic relationship can be beneficial for both the fungus and the plant. The fungi receive nutrients and a protected environment, while the plants may benefit from improved resistance to pathogens, enhanced growth, and increased tolerance to environmental stress. Fungal endophytes are known to produce a variety of bioactive compounds, which are molecules that can have a significant impact on living organisms, including potential medicinal and agricultural applications. Here are some examples of bioactive compounds produced by fungal endophytes. Research in this field is ongoing, and scientists are continually discovering new bioactive compounds from fungal endophytes. Sulfur-containing compounds are a diverse group of molecules that contain sulfur atoms in their chemical structure. Sulfur is an essential element for life, and it plays crucial roles in various biological processes. Thus, this chapter discusses the production of sulfur-containing compounds from endophytic fungi. Also, it shows different groups of sulfur-containing compounds that have different biological applications. Finally, displays different biological applications, e.g., antimicrobial as well as anticancer activities.