Pest management is a critical component of aquaculture operations since high stocking densities can facilitate rapid pest infestation and high stock losses. The Acropora eating-flatworm, Prosthiostomum acroporae impact the health of captive Acropora colonies, which are commonly grown as part of coral aquaculture for trade, research and the hobbyist sector. We investigated the efficacy of anthelmintics levamisole and praziquantel for the removal of Acropora-eating flatworms from A. millepora using one-hour chemical immersions and assessed if these treatments negatively impacted coral growth and/or caused bleaching. Coral fragments (194 total) were spread across eight treatments; levamisole infested (LI; n = 20), levamisole uninfested (LU; n = 20), praziquantel (in EtOH) infested (PI; n = 20), praziquantel (in EtOH ) uninfested (PU; n = 20), handling control infested (HCI; n = 14), handling control uninfested (HCU; n = 20), EtOH control (EC; n = 40), control with no handling (NHC; n = 40). To test the efficacy of flatworm removal by short, one-hour chemical immersions, A. millepora fragments (54 total) were manually infested (three P. acroporae per fragment) and immersed separately to uninfested A. millepora fragments (60 total). All fragments were shaken in in a bath of seawater following immersion, then mechanically screened to recover any flatworms not removed from either immersion or shaking to determine the removal efficacy of the treatments. Furthermore, coral fragments (194 total) were photographed before treatment and four weeks following treatments to compare coral basal growth and visual signs of bleaching between infested and uninfested fragments. Levamisole and praziquantel immersions removed significantly more flatworms from A. millepora fragments (93% ± 3.8 and 95.0% ± 2.6 respectively; mean ± SE; p < 0.05) compared to the handling control (26% ± 7.5%). Chemical treatments had no significant effect on basal growth, with fragments across all treatments (including controls) increasing basal area by 73.31 ± 3.82% (mean ± SE). Furthermore, bleaching was not observed for any A. millepora fragments across the treatments and controls. Results from this study demonstrate that levamisole and praziquantel used in conjunction with water movement were effective at removing >90% of Acropora eating-flatworms with no observable negative impacts on coral health on treated coral fragments relative to controls.