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Aquatic contamination from the accumulation of pharmaceuticals has induced severe toxicological impact to the ecological environment, especially from non-steroidal anti-inflammatory drugs (NSAIDs). Real-time monitoring of flutamide, which is a class of NSAIDs, is very significant in environmental protection. In this work, we have synthesized the hexagonal-h boron nitride decorated on bismuth oxide (Bi2O3/h-BN) based nanocomposite for the effective electrochemical detection of flutamide (FTM). The structural and morphological information of the heterostructured Bi2O3/h-BN nanocomposite was analyzed by using a sequence of characterization methods. Voltammetric techniques were used to evaluate the analytical performance of the Bi2O3/h-BN modified screen-printed carbon electrode (SPCE) for the FTM detection. The Bi2O3/h-BN modified SPCE displays a synergetic catalytic effect for the reduction of FTM due to large surface area, numerous active sites, fast charge transfer and abundant defects. The proposed electrochemical sensing platform demonstrates high selectivity, low detection limit (9.0 nM), good linear ranges (0.04–87 μM) and short response time for the detection of FTM. The feasibility of the electrochemical sensor has been proved by the successful application to determine FTM in environmental samples.