The polychlorinated dibenzo-p-dioxins/furans (PCDD/Fs) and dioxin-like polychlorinated biphenyls (dl-PCBs) are worldwide contaminants, and they tend to accumulate in wide variety of matrices. Therefore, due to the highest accumulation rate and recalcitrancy, their precise quantification makes significant concern about their toxicological effects on both humans and organisms. The objective of the study is that using hydrogen carrier gas instead of helium in gas chromatography with triple quadrupole (GC-MS/MS) systems could contribute to improvements on the analysis of dl-PCBs and PCDD/Fs in environmental matrices. The study evaluates the performance of the analysis time under the desired chromatographic resolution criteria for PCDD/Fs analysis, monitoring the plausible mass spectrum/fragmentation ratio changes, and finally the quantification limits of the targeted most toxic persistent organic compound congeners. The main advantage of using H2 carrier gas is that the analysis time was drastically reduced (∼2.5 times) along with improved resolution due to an increase in peak widths in ∼0.6-0.7 factor. This study emphasized that the resolution was remarkably affected by the hexa congeners of PCDD/Fs; nearly baseline separation was observed. However, the sensitivity was slightly reduced (∼6-7 fold), which affected the calibration starting concentrations (0.8-3.2 pg/μl). The acquired mass spectra indicated that the lower fragment enhancement was noticeable, particularly on higher chlorinated ones (hexa, hepta, and octa congeners). The calculated ortho-effect values (1-58) in this study are consistent with the previous results in the literature (1-66 and 1-83) and supports the conclusion about the observations of lower fragment enhancement. Despite non-detection of hydrogenation, there is a significant difference in the quant/qual ion ratios in the studied compounds between helium and hydrogen carrier gas. The finalized methodology was examined, and the performance of the hydroinert® ion source was assessed over a three-month analysis period with a real sample analysis (RSD ≤17.8 %). The results indicate that hydrogen is a potential and reliable GC-MS/MS carrier gas in dl-PCBs and PCDD/Fs for environmental matrices.