A copper ion-doped clinoptilolite-modified carbon paste electrode was evaluated as an amperometric sensor for non-electroactive ammonium cations in flow injection analysis. The electrochemical activity of copper was prevented in electrolyte solutions containing size-excluded cations such as tetrabutylammonium, while the presence of non-size-excluded cations such as ammonium gave rise to appreciable responses. Consequently, the injection of ammonium samples at the electrode surface (into a carrier stream made of tetrabutylammonium bromide solution) resulted in peak currents proportional to the concentration of the analyte NH4+. After optimisation of the experimental conditions, very reproducible results (standard deviations <1%, n=10) were obtained, linear calibration was achieved in the 2×10−5 M to 1×10−3 M concentration range, and the detection limit was 5×10−6 M. The effect of interfering cations was also discussed and the sensor's performance was evaluated for the analysis of ammonium in synthetic ground water.