An analytical method that utilizes isotope-dilution gas chromatography-mass spectrometry (ID-GC–MS) coupled with injection-port butylation was developed. The method was validated, and confirmed to be able to determine the presence of three commonly detected endocrine-disrupting chemicals (EDCs: 4-tert-octylphenol (4-t-OP), 4-nonylphenols (4-NPs) and bisphenol A (BPA)) in human urine with high precision and accuracy. After sample preparation by solid-phase extraction, the extract was introduced into GC–MS via injection-port butylation. The butylated target analytes were identified and quantified by using ion-trap mass spectrometry operating in the selected-ion-storage mode, and employing the measurement of peak area ratios of the butylated target analytes and labeled-analogues in the samples and calibration standards. The labeled-analogues were also used to correct the variations associated with the analysis and matrix effect. The limits of quantitation (LOQs) ranged from 0.1 to 0.3 ng/mL. High precisions for both intra- and inter-day analysis ranged from 1 to 6%, and excellent accuracy (mean recovery) ranged from 92 to 105% on two concentration levels. In human urine, the total concentrations of three selected EDCs varied from 1.28 to 7.14 ng/mL. 4-NPs were detected within all collected samples. The developed method allows accurate analysis of trace-level of EDCs in urine, and these target EDCs could act as useful biomarkers to assess exposure in biomonitoring studies and programs.