This paper explores the potential of applying reversed-phase sequential injection chromatography (SIC) to determine the anticoccidial agents Lasalocid and Toltrazuril in various matrices including ground water, pharmaceutical formulations and feed. SIC was performed by connecting a 25 × 4.6 mm monolithic C18 column to a 2 m long pathlength capillary flow cell, where the usage of a flow cell lowers the detection limit compared to a conventional short-distance flow cell, providing a simple detection system for these two compounds which are initially poorly UV absorbents. The proposed set-up provides a high injection throughput of 12 h − 1 , as well as a limit of detection of 0.019 and 0.010 mg/L for Toltrazuril and Lasalocid, respectively. The repeatabilities obtained (n = 10) were lower than 2% and 4% for Toltrazuril and Lasalocid, respectively.