Several studies investigating the prevention and treatment of external parasites in farmed olive flounder Paralichthys olivaceus have found that the anticoccidial agent toltrazuril sulfone is an effective antiparasitic. Prior to undertaking a full-scale study, we developed analytical methods to detect the levels of toltrazuril and toltrazuril sulfone in farmed flounder samples using liquid chromatography-electrospray ionization tandem mass spectrometry (LC-MS/MS). This analysis showed that LC-MS/MS changed the mobile phase and collision energy of toltrazuril and toltrazuril sulfone. This was validated using established conditions. Sample pre-treatment for this process involved extraction with dichloromethane and purification by liquid-liquid extraction in formic acid, acetonitrile, and h-hexane, followed by determination of all compounds by LC-MS/MS. Separation was achieved within 10 min by gradient elution using a Capcell Pak C18 (3.0 μm, 100×2.0 mm) analytical column (Shiseido UG 120V) with a mixture of 0.1% (v/v) formic acid and acetonitrile. Multiple reaction monitoring was used for selective detection of toltrazuril and toltrazuril sulfone. This method yields satisfactory results for linearity, precision, and limits of quantification. Therefore, the method established in our study will serve as a basis for further research on parasite control by toltrazuril and toltrazuril sulfone.