Hydrogen is an excellent alternative energy source, particularly for vehicles. Despite the expansion of a considerable number of infrastructures, such as hydrogen refueling stations, there is a lack of efficient inspection methods for monitoring the hydrogen fuel quality. In this study, a hydrogen impurity analyzer (HIA) based on mobile gas chromatography with a thermal conductivity detector is developed and evaluated for the quality assurance of hydrogen fuel. Accordingly, O2, N2, and Ar which help in monitoring air leaks at hydrogen refueling stations, and CH4, which can also be detected by HIA, are selected as target impurities. The HIA reached limits of detection of 2.93, 0.72, 0.84, and 1.54 μmol/mol for O2, Ar, N2, and CH4, respectively. Moreover, the ISO 14687 requirements are satisfied with respective HIA expanded uncertainties of 2.6, 8.7, 8.2, and 9.4% (coverage factor k = 2). The developed system is ISO-compliant and offers enhanced mobility for online inspections.