Fungal endophytes are microorganisms that live in plants’ tissues without causing any major harm. They were found to be very diverse and highly beneficial for the health and growth of their host plants. This has driven attention to potential of fungal endophytes that are generating a lot of interest from various sectors such as agriculture, industrial, and pharmaceutical, where it is believed that fungi can produce multiple bioactive molecules. Some screening and isolation methods have demonstrated the diversity of secondary metabolites synthesized by them. From this study, the results showed that bioactive compounds secreted by fungal endophytes have antibacterial, antioxidant, anticancer, insecticidal properties, etc., while also indicating their usefulness in biotechnology applications such as agriculture or medicine manufacture. Finally, the production of biologically active materials by these fungi can be useful for biotechnological processes including agriculture or drugs preparation. Consequently, it is stated that fungal endophytes are capable of accumulating a vast array of novel bioactive compounds. This review paper focuses on two topics: diversification of fungal endophytes and biosynthetic pathways for bioactive molecules.