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Hypersonic aircraft flying at Mach 5 to 8 are a means for travelling very long distances in extremely short times and even significantly faster than supersonic transport (Mach 1.5 to 2.5). Fueled with liquid hydrogen (LH2) their emissions consist of water vapour (H2O), nitrogen oxides (NOx) and unburnt hydrogen. If LH2 is produced in a climate- and carbon neutral manner, carbon dioxide does not have to be included when calculating the climate footprint. While H2O that is emitted near the surface has a very short residence time (hours) and thereby no considerable climate impact, super- and hypersonic aviation emit at very high altitudes (15 km to 35 km), with residence times of months to several years, and therefore the emitted H2O has a substantial impact on climate via high altitude H2O changes. Since the (photo-)chemical lifetime of H2O is largely decreasing at altitudes above 30 km via the reaction with O(1D) and via photolysis, one could speculate that H2O climate impact from hypersonics flying above 30 km becomes smaller with higher cruise altitude. Here we use two state-of-the-art chemistry-climate models and a climate response model to investigate atmospheric changes and respective climate impacts due to two potential hypersonic fleets flying at 26 km and 35 km, respectively. We show for the first time that the (photo-)chemical H2O depletion at high altitudes is overcompensated by a recombination of hydroxyl radicals to H2O and an enhanced methane depletion, leading to an increase in H2O concentrations. This results in a steady increase of the H2O perturbation lifetime of up to 4.41 ± 0.20 years at 35 km. We find a 0.083 ± 0.014 % and 0.16 ± 0.015 % depletion of the ozone layer and a 43.0 ± 4.8 Tg and 94.0 ± 4.5 Tg increase in stratospheric H2O due to the two hypersonic fleets flying at 26 km and 35 km respectively. Our calculations show that the climate impact of hypersonic transport is estimated to be roughly 8–20 times larger than a subsonic reference aircraft with the same transport volume (revenue passenger kilometers) and that the main contribution stems from H2O.