Protozoan parasites can cause serious infections that affect millions of people around the globe especially in resource-limited areas, conflict zones, and hard-to reach-regions. These infections pose a huge health, social, and economic threat to prevalent countries as control of protozoan diseases is quite challenging. Despite most protozoal infections been curable, few antiprotozoal drugs are available, and some tend to be toxic to humans and animals due to physiological similarities with targeted parasites. Plants are a rich source of natural compounds that possess different antimicrobial effects and can serve as alternative antiprotozoal agents. This chapter discusses the secondary metabolites of plants and how they are potential candidates to treat a series of protozoan infections.