The determination of urinary S‐phenylmercapturic acid (S‐PMA) represents the most reliable biomarker to monitor the intake risk of airborne benzene. Recently, the European CHemical Agency (ECHA) deliberate new occupational exposure limits for benzene, recommended a S‐PMA Biological Limit Value of 2 μg/g creatinine. This limit is an order of magnitude lower than the previous one and its determination constitutes a challenge in the analytical field. We developed and validated a method, that allows the fully‐automated and sensitive determination of S‐PMA by the use of gas‐chromatography negative chemical ionization tandem mass spectrometry in isotopic dilution. For NCI we selected a mixture of 1% isobutane in argon as reactive gas, by studying its chemical ionization mechanism and optimal parameters compared to pure isobutane or pure methane. This gas mixture produces a more abundant signal of the target analyte than isobutane or methane and it extended the operative lifetime of the ion source, enabling us to start an high throughput approach of the S‐PMA anlysis. Moreover, energy resolved mass spectrometry experiments were carried out to refine the MS/MS analysis conditions, testing nitrogen and argon as collision gas. The method optimization was pursued by a chemometrich model by using the experimental design. The quantification limit for S‐PMA was 0.10 μg/L. Accuracy (between 98.3% to 99.6 %) and precision (ranging to 1.6% to 6.4%) were also evaluated. In conclusion, the newly developed assay represent a powerfull tool for the robust, reliable and sensitive quantification of urinary S‐PMA and, due to its automation, it is well suited for application in large environmental and biological monitoring.