To detect and characterise compounds in complex matrices, it is often necessary to separate the compound of interest from the matrix before analysis. In our previous work, we have developed the coupling of supercritical fluid chromatography (SFC) with nuclear magnetic resonance (NMR) spectroscopy for the analysis of nonpolar samples [Van Zelst et al., Anal. Chem., 2018, 90, 10457]. In this work, the SFC-NMR setup was successfully adapted to analyse polar samples in complex matrices. In-line SFC-NMR analysis of two N-acetylhexosamine stereoisomers was demonstrated, namely N-acetyl-mannosamine (ManNAc) and N-acetyl-glucosamine (GlcNAc). ManNAc is a metabolite that is present at elevated concentrations in patients suffering from NANS-mediated disease. With our SFC-NMR setup it was possible to distinguish between the polar stereoisomers. Until now, this was not possible with the standard mass-based analysis techniques. The concentrations that are needed in the SFC-NMR setup are currently too high to be able to detect ManNAc in patient samples (1.7 mM vs. 0.7 mM). However, several adaptations to the current setup will make this possible in the future.