Emerging infectious diseases in marine systems threaten food security and ecosystem function. Experiments to determine drivers of transmission and mortality from emerging pathogens require a reliable supply of disease-free animals. Imperfect detection of subclinical, latent, and early stage infections, however, necessitates effective treatments to remove infection from animals with unknown infection status. In this study, a procedure utilizing elevated temperatures and over-the-counter parasiticides to remove Hyalophysa lynni was developed. The apostome ciliate H. lynni is responsible for shrimp black gill (sBG) disease in commercially important southeastern shrimp fishery species, including Litopenaeus setiferus (white shrimp). Following a series of pilot studies to determine parasiticides combination and dosage, L. setiferus of unknown infection status were exposed to either 20°C or 30°C artificial seawater, and a parasiticide cocktail of metronidazole (3.15 mg L–1) and Cu+2 (0.5 mg L–1) or a medication-free control for 14 days in a fully crossed experimental design. All treatments, except for the 20°C without medications treatment, significantly reduced pathogen prevalence. The 30°C artificial seawater with parasiticide treatment resulted in complete curing of the experimental population, but shrimp mortality in this treatment was high (50%). This high mortality may have contributed to the low parasite prevalence found in this treatment by differentially culling infected individuals. If this is the case, the parasiticides may lower the parasite prevalence both by curing infections and heightening stress and subsequent mortality of diseased individuals. Although this procedure was developed to produce H. lynni-free shrimp to facilitate experimental studies of sBG disease, it is likely that this methodology would effectively produce specific-pathogen-free individuals in other crustacean species.