Endophytes are a group of microbes residing mutually within the tissues of their host plant without causing any overt symptoms. Secondary metabolites produced by fungal endophytes are used in the treatment of many diseases including protozoan diseases like malaria and visceral leishmaniasis (also known as kala-azar). These two parasitic diseases together cause mortality and morbidity to millions of people globally. There are drugs available to treat these diseases, but the increasing resistance among the protozoan parasite to present-day drugs has driven the scientific community in search of novel sources of pharmacologically active compounds of therapeutic value, and medicinal plants derived from fungal endophytes have shown substantial potential for this cause. Compounds like Taxol, quinine, cytochalasins, cyclodepsipeptide, fusaripeptide A, cochlioquinone A, purpureone, isocochlioquinone A, citrinin, terrenolide S, and curvulin derived from fungal endophytes have been used for their anti-plasmodial and antileishmanial property, respectively. This book chapter reviews natural bioactive compounds derived from fungal endophytes with various antiparasitic biological activities.