A rapid and accurate ion chromatography (IC) method (limit of detection as low as 0.06 mg L−1) for fosfomycin concentration determination in pharmaceutical industrial wastewater was developed. This method was compared with the performance of high performance liquid chromatography determination (with a high detection limit of 96.0 mg L−1) and ultraviolet spectrometry after reacting with alizarin (difficult to perform in colored solutions). The accuracy of the IC method was established in the linear range of 1.0–15.0 mg L−1 and a linear correlation was found with a correlation coefficient of 0.9998. The recoveries of fosfomycin from industrial pharmaceutical wastewater at spiking concentrations of 2.0, 5.0 and 8.0 mg L−1 ranged from 81.91 to 94.74%, with a relative standard deviation (RSD) from 1 to 4%. The recoveries of effluent from a sequencing batch reactor treated fosfomycin with activated sludge at spiking concentrations of 5.0, 8.0, 10.0 mg L−1 ranging from 98.25 to 99.91%, with a RSD from 1 to 2%. The developed IC procedure provided a rapid, reliable and sensitive method for the determination of fosfomycin concentration in industrial pharmaceutical wastewater and samples containing complex components.