The increasing demand for sustainable air mobility has led to the development of innovative aircraft designs, necessitating a balance between environmental responsibility and profitability. However, despite technological advancements, there is still limited understanding of the maintenance implications for hydrogen systems in aviation. The aim of this study is to estimate the maintenance costs of replacing the hydrogen storage system in an aircraft as part of its life cycle costs. To achieve this, we compared conventional and hydrogen-powered aircraft. As there is insufficient data for new aircraft concepts, typical probabilistic methods are not applicable. However, by combining global sensitivity analysis with Dempster–Shafer Theory of Evidence and discrete event simulation, it is possible to identify key uncertainties that impact maintenance costs and economic efficiency. This innovative framework offers an early estimate of maintenance costs under uncertainty, enhancing understanding and assisting in decision-making when integrating hydrogen storage systems and new aviation technologies.