Ion mobility spectrometry provides ion separation in the gas phase mainly based on differing ion-neutral collision cross sections, enabling powerful analysis of many isomers. However, the separation also has a miniscule mass dependence due to the acceleration and collision properties. In this work, we show for the first time that using a compact ultra-high-resolution ion mobility spectrometer with a resolving power of 250 and an UV ionization source enables the separation of isotopologues with ion mobility spectrometry. This is demonstrated for regular and perdeuterated acetone, benzene, and toluene as well as toluene-13C7 in nitrogen and in purified air as drift gas. The observed peak shifts in the ion mobility spectrum agree with the basic ion mobility equation when using nitrogen as drift gas and also agree with a combination of this equation with Blanc’s law when using purified air as drift gas. For benzene and toluene, a reduction in the ion-neutral collision cross section of the isotopically replaced species is observed. Furthermore, a third peak formed from regular and perdeuterated acetone is observed, which can most likely be attributed to the exchange of a methyl group.