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Human milk oligosaccharides (HMOs) are an important class of biomolecules responsible for the healthy development of the brain‐gut axis of infants. Unfortunately, their accurate characterization is largely precluded due to a variety of reasons – there are over 200 possible HMO structures whereas only 10s of these are available as authentic analytical standards. Furthermore, their isomeric heterogeneity stemming from their many possible glycosidic linkage positions and corresponding α/β anomericities further complicates their analyses. While liquid chromatography coupled to tandem mass spectrometry remains the gold standard for HMO analyses, it often times cannot resolve all possible isomeric species and thus warrants the development of other orthogonal approaches. High‐resolution ion mobility spectrometry coupled to mass spectrometry has emerged as a rapid alternative to condensed‐phase separations but largely has remained limited to qualitative information related to the resolution of isomers. In this work, we have assessed the use of permethylation to improve both the resolution and sensitivity of HMO analyses with cyclic ion mobility separations coupled with mass spectrometry. In addition to this, we have developed the first‐ever high‐resolution collision cross‐section database for permethylated HMOs using our previously established calibration protocol. We envision that this internal reference database generated from high‐resolution cyclic ion mobility spectrometry‐mass spectrometry will greatly aid in the accurate characterization of HMOs and provide a valuable, orthogonal, approach to existing liquid chromatography–tandem mass spectrometry‐based methods. [ABSTRACT FROM AUTHOR]