Regions with a tropical climate are frequently affected by endemic diseases caused by pathogenic parasites. More than one billion people worldwide are exposed directly to tropical parasites. The literature cites several antiparasitic metabolites obtained from medicinal plants or via synthetic pathways. However, fungi produce a diversity of metabolites that play important biological roles in human well-being. Thus, they are considered a potential source of novel natural agents for exploitation in the pharmaceutical industry. In this brief review article, we will provide an overview of the current situation regarding antiparasitic molecules derived from filamentous fungi, in particular, those which are effective against protozoan parasites, such as Plasmodium, Trypanosoma, and Leishmania, vectors of some neglected tropical diseases. Diseases and parasitic agents are described and classified, and the antiparasitic properties of natural compounds produced by the fungi of the phyla Basidiomycota and Ascomycota are reviewed herein, in order to explore a topic only sparsely addressed in the scientific literature.