Endophytes, including bacteria and fungi, can colonize the inner tissues of all plants. Since some endophytes do not remain as endophytes throughout their life cycle, they are not fully understood. In recent years, endophyte fungi have been considered because of their potential reliable compounds and economic properties. Alkaloids are naturally occurring chemicals with useful physiological and pharmacodynamic effects. Alkaloid drugs exhibit bioactive properties such as fungicidal, antibacterial, and anticancer actions. The most important fungal alkaloids are indole, ergot, pyrrolizidine, and imidazole. Endophytic fungal alkaloids have several potential applications. Considering current understanding, this chapter provides detailed information regarding endophytic fungal alkaloids.