Neuropathogenic protozoa have evolved strategies to breach the blood-brain barrier and invade the central nervous system. These include transcellular, paracellular and the Trojan horse routes but the associated molecular mechanisms remain incompletely understood. Here, we summarize the current understanding of protozoa penetration across the blood-brain barrier, focusing on Plasmodium, Babesia, Trypanosoma, Toxoplasma, Acanthamoeba and Balamuthia. Advances in understanding the molecular pathways will offer opportunities for the rational development of novel therapeutic interventions.