The goal of the study was to investigate the retention mechanism of selected fungicides in hydrophilic interaction liquid chromatography (HILIC) and per aqueous liquid chromatography (PALC). Chromatographic measurements were made on four physicochemically diversified HILIC columns, which were evaluated for the analysis of nine biologically active compounds, such as strobilurins and triazoles. The effects of the operating conditions on separations were investigated, including the concentration of the organic solvent in the aqueous-organic (acetonitrile) mobile phase. The results were compared, and it was shown that two different retention mechanisms dominate in PALC at low acetonitrile concentrations and in HILIC at high acetonitrile concentrations.