Post-translational modifications are a regulatory mechanism for fine-tuning protein localisation and function. S-palmitoylation is a reversible lipid modification that causes an increased affinity for membranes in its substrates. S-palmitoylation has been found in recent years to have a wide-ranging impact on protein dynamics in eukaryotic cells. We investigated depalmitoylation, and the validity of targeting this process with inhibitors to disrupt the lifecycle of Apicomplexans, organisms that cause severe morbidity and mortality globally. We identified a family of enzymes with the potential for depalmitoylation activity. One of these, PPT1, a close homologue of depalmitoylating enzymes that have been characterised in other eukaryotic organisms, was shown to be active but dispensable for parasite survival in vitro. Inhibitors designed to block depalmitoylation were toxic to parasites but were shown to target a number of other proteins including the three other candidates for depalmitoylation activity that could be compensating for the loss of PPT1.