Urocanic acid (UCA) has been reported to be a mast cell degranulator and has also been suggested as a complementary agent in implicated scombroid fish poisoning. In this research, a new method is described to extract, clean up and perform simultaneous ion-pair chromatographic analysis of trans- and cis-urocanic acid (UCA) in fish samples. UCA was extracted using 0.05 M HCl and protein was removed from the extract by precipitation with 10% trisodium citrate and 10% citric acid. The HPLC method that is developed showed a rapid, precise and sensitive method with short retention time for simultaneous separation of UCA isomers in fish samples. Estimation of trans- and cis-UCA in the muscle of Indian mackerel, tuna and sardine showed that, as expected, no cis-UCA existed in fish muscles and the highest concentration of trans-UCA was found in Indian mackerel with 118.8 mg kg⁻¹ while the highest concentrations of trans-UCA in tuna and sardine were 12.1 and 17.5 mg kg⁻¹, respectively.