The mitochondrial electron transport chain (ETC) of apicomplexan parasites differs considerably from the ETC of the animals that these parasites infect, and is the target of numerous anti-parasitic drugs. The cytochromecoxidase complex (Complex IV) of the apicomplexanToxoplasma gondiiETC is more than twice the mass and contains subunits not found in human Complex IV, including a 13 kDa protein termedTgApiCox13.TgApiCox13 is homologous to a human iron-sulfur (Fe-S) cluster-containing protein called the mitochondrial inner NEET protein (HsMiNT) which is not a component of Complex IV in humans. Here, we establish thatTgApiCox13 is a critical component of Complex IV inT.gondii, required for complex activity and stability. Furthermore, we demonstrate thatTgApiCox13, like its human homolog, binds two Fe-S clusters. We show that the Fe-S clusters ofTgApiCox13 are critical for ETC function, having an essential role in mediating Complex IV integrity. Our study provides the first functional characterisation of an Fe-S protein in Complex IV.