This study aims to determine the mass balance of chlorpheniramine hydrochloride (ROBH) in the body of Channel catfish (Ictalurus punctatus). ROBH was administered orally at a dose of 20 mg/kg; following drug administration, the water samples were collected at predetermined time points (12, 24, 48, 72, 96, 120, 144, and 168 h), the experimental fish were executed after the water samples were obtained at 168 h, and the tissue samples were collected separately from the bones. The water and tissue samples were analyzed by high-performance liquid chromatography coupled with tandem mass spectrometry (HPLC–MS/MS) for concentrations of ROBH and its potential major metabolites, 4-chlorohippuric acid (PCHA) and 4-chlorobenzoic acid (PCBA). The tissue samples were prepared using a modified QuEChERS procedure; the water samples were prepared using a liquid–liquid extraction (LLE) procedure. The results show that the recovery rate of ROBH in fish is very low, less than 2% of the total amount of the drug, and the recovery in water can reach 80.7% of the total amount of the drug. The content of PCBA accounted for 42.4% of the total amount of the drug; the content of ROBH accounted for 38.3% of the total amount of the drug. The content of PCHA accounted for less than 1% of the total amount of the drug. The results show that, after a single administration, ROBH is rapidly metabolized in vivo and excreted in the form of ROBH as well as metabolite PCBA. ROBH and PCBA can be used as the main targets for the metabolism detection of ROBH in Channel catfish.