The Life Cycle Assessment (LCA) methodology is often used to check the environmental suitability of hydrogen energy systems, usually involving comparative studies. However, these comparative studies are typically affected by inconsistent methodological choices between the case studies under comparison. In this regard, protocols for the harmonisation of methodological choices in LCA of hydrogen are available. The step-by-step application of these protocols to a large number of case studies has already resulted in libraries of harmonised carbon, energy, and acidification footprints of hydrogen. In order to foster the applicability of these harmonisation protocols, a web-based software for the calculation of harmonised life-cycle indicators of hydrogen has recently been developed. This work addresses—for the first time—the validation of such a tool by checking the deviation between the available libraries of harmonised carbon, energy, and acidification footprints of hydrogen and the corresponding tool-based harmonised results. A high correlation (R2 > 0.999) was found between the library- and tool-based harmonised life-cycle indicators of hydrogen, thereby successfully validating the software. Hence, this tool has the potential to effectively promote the use of harmonised life-cycle indicators for robust comparative LCA studies of hydrogen energy systems, significantly mitigating misinterpretation.