The goal of this study was to qualify gas chromatography coupled to atmospheric pressure ionization tandem mass spectrometry (APGC-MS/MS) as a reliable and valid technique for analysis of halogenated dioxins and furans that could be used in place of more traditional gas chromatography coupled to high-resolution mass spectrometry (GC-HRMS) analysis. A direct comparison of the two instrumental techniques was performed. APGC-MS/MS system sensitivity was demonstrated to be on the single femtogram level. The APGC-MS/MS analysis also demonstrated method detection limits (MDLs) in both sediment and fish that were 2-18 times lower than those determined for the GC-HRMS. Inlet conditions were established to prevent issues with sample carry-over, due largely to the enhanced sensitivity of this technique. Additionally, this work utilized direct injection for sample introduction through the split/splittless inlet. Finally, quantification of both sediment and fish certified reference materials were directly compared between the APGC-MS/MS and GC-HRMS. The APGC-MS/MS performed similarly to, if not better than, the GC-HRMS instrument in the analysis of these samples. This data is intended to substantiate APGC-MS/MS as a comparable technique to GC-HRMS for the analysis of dioxins and furans.