Abstract The thermal reactions of methane with the oxygen‐rich cluster cations [Si2O5]⋅+ and [Si2O5H2]⋅+ have been examined using Fourier transform–ion cyclotron resonance (FT‐ICR) mass spectrometry in conjunction with state‐of‐the‐art quantum chemical calculations. In contrast to the inertness of [Si2O5].+ towards methane, the hydrogenated cluster [Si2O5H2].+ brings about hydrogen‐atom transfer (HAT) from methane with an efficiency of 28 % relative to the collision rate. The mechanisms of this process have been investigated in detail and the reasons for the striking reactivity difference of the two cluster ions have been revealed.