We attempted to apply the HACCP system adopted in the food industry to a olive flounder (Paralichthys olivaceus) aquaculture farm to ensure the hygiene safety of farmed fish. In this study, HACCP system procedures, including HACCP team organization, critical point determination, establishment of standard limits etc., were established using Codex 12 procedures. To determine whether hazards were critical elements, we evaluated the likelihood and seriousness of each hazard element. The likelihood of residual medicine exceeding the acceptable limit in shipped fish products was demonstrated to be a critical hazard element. Management of the shipment stage was determined to be a critical control point (CCP). Checking the records for stock and release and maintaining a history of medicine use before shipping the fish were suggested as monitoring methods. The standards for acceptable residual medicine were set based on relevant laws and regulations, and then the limits were adapted and established for the CCP. An HACCP plan applicable to olive flounder farms was established.