The olive flounder (Paralychthys olivaceus) is a representative farmed fish species in South Korea, which is cultured in land-based tanks and accounts for approximately 50% of total fish farming production. However, farmed olive flounder are susceptible to infection with parasitic scuticociliates, which cause scuticociliatosis, a disease resulting in severe economic losses. Thus, there has been a longstanding imperative to develop a highly stable and effective antiparasitic drug that can be rapidly administered, both orally and by bath, upon infection with scuticociliates. Although the efficacy of commercially available mebendazole (MBZ) has previously been established, this compound cannot be used for olive flounder due to hematological, biochemical, and histopathological side effects. Thus, we produced material remediated mebendazole (MR MBZ), in which elements comprising the molecule were remediated by using full-overlapped gravitational field energy, thereby reducing the toxicity of the parent material. The antiparasitic effect of MR MBZ against scuticociliates in olive flounder was either similar to or higher than that of MBZ under the same conditions. Oral (100 and 500 mg/kg B.W.) and bath (100 and 500 mg/L) administrations of MBZ significantly (p < 0.05) increased the values of hematological and biochemical parameters, whereas these values showed no increase in the MR MBZ administration group. In addition, there were no histopathological side effects, such as atrophic degeneration or hyaline droplet degeneration, whereas these were observed when MBZ was administered. Thus, we report that the material remediation method using full-overlapped gravitational field energy can be used to reduce drug toxicity.