Hydrogen fuel, which is essential for the hydrogen economy, including hydrogen cell vehicles, must be of high quality for optimal hydrogen cell use. Currently, hydrogen fuel quality control is mainly done by offline analysis with periodic sampling. However, with the anticipated surge in hydrogen charging stations, there's a pressing need for cost-effective, high-throughput online analysis systems. Additionally, the miniaturization of these analytical instruments for field application is also a challenge. In this study, we present a compact, real-time hydrogen fuel analyzer based on gas chromatography with a pulsed discharge helium ionization detector. Its dual-column system efficiently analyzes major impurities in hydrogen fuel in less than 30 min. Indicator species (CO, CO2, CH4, O2, N2, and additional hydrogen sulfide [H2S]) are determined by examining hydrogen production and supply processes. The analyzer's measurement capability is consistent with µmol/mol-level analysis, providing valuable real-time information for hydrogen infrastructure managers. Additionally, it can analyze H2S, a crucial marker of sulfur compounds acting as catalytic poisons in fuel cells. This real-time analyzer offers efficient, informed decision-making support for hydrogen infrastructure managers, enhancing the overall reliability of hydrogen fuel in fuel-cell electric vehicles.