Fungal endophytes are microorganisms that can be neutral, commensal, or beneficial, as well as dormant saprobes and pathogens in the latent phase of their life cycle, and can be isolated from asymptomatic plant tissues. Additionally, endophytes seem to be closely associated with different parts of their host plants and can produce various bioactive natural products. Plants that are from unique environmental settings are endemic, have unusual longevity, develop in areas of great biodiversity, and are interesting targets for the recovery of unique endophytic species capable of producing bioactive compounds. Considering that the fungal communities associated with most plants in Neotropical environments have not yet been investigated, they represent an untapped source of secondary metabolites that may be useful in the development of new and safe compounds beneficial for human health. New strategies can be adopted to recover endophytic species from cryptic and rare Neotropical host plants that can produce novel structural scaffolds. Threats such as cancer, infectious fungi and bacteria, and causative agents of neglected tropical diseases continue to demand special attention and research investment due to their associated high mortality rates, drug resistance, or lack of effective and safe therapeutics. In this chapter, we focus on fungal endophytes and their compounds recovered from Neotropical plants that were evaluated for their antibacterial, antifungal, antiparasitic, antitumor, and antiviral activities.