Apicomplexan parasites such as Plasmodium falciparum, the causative agent of malaria, contain a non-photosynthetic plastid known as the apicoplast that functions to produce essential metabolic compounds. It was previously reported that several members of the Clp family of chaperones and proteases localize to the apicoplast. In bacteria and in chloroplasts these proteins form complexes that degrade proteins in a proteasome-like manner to regulate key cellular processes, but their function in the apicoplast is completely unknown. In this study, we generated a conditional mutant of the P. falciparum apicoplast-targeted pfclpc gene and found that under normal conditions it localizes to the apicoplast. Knockdown of PfClpC results in growth inhibition and morphological defects, indicating that PfClpC is essential for parasite viability. Upon inhibition, PfClpC loses its apicoplast localization and appears in vesicle-like structures. Other apicoplast-targeted proteins also localize to these structures, suggesting that organelle integrity is compromised. Addition of isopentynyl pyrophosphate completely rescued the growth inhibition, indicating that the only essential function of PfClpC is related to the apicoplast. Moreover, cellular assays suggest that PfClpC inhibition interferes with the ability of the schizont-stage parasites to properly sort functional apicoplast organelles into daughter-merozoites. These data show that PfClpC is an essential gene that functions to maintain apicoplast integrity.