Apicomplexan parasites encompass a diverse group of eukaryotic intracellular pathogens that infect various animal hosts to cause disease. Intriguingly, apicomplexans possess a unique organelle of algal origin, the apicoplast, which phylogenetically links these parasites to dinoflagellates and photosynthetic, coral-associated organisms. While production of secondary metabolites in closely related organisms has been thoroughly examined, it remains widely unexplored in apicomplexans. In this Perspective, we discuss previous work toward understanding secondary metabolite building block biosynthesis in apicomplexans and highlight the unexplored enzymology and biosynthetic potential of these parasites in the context of evolution.