Nicotine and cotinine are very polar basic molecules, which makes it difficult to analyze them by reversed-phase liquid chromatography (RPLC), especially in biological samples. Additives with an ionic character have been traditionally used in RPLC as silanol suppressors. The aim of our study was to investigate the potential of selected ionic liquids in improving chromatographic performance in comparison with common additives. The experimental design was conducted using the following ionic liquids as the mobile phase modifiers: 1-butyl-3-methylimidazolium tetrafluoroborate, BMIM[BF4] and 1-butyl-3-methylimidazolium hexafluorophosphate BMIM[PF6], with a C18 chromatographic column. The separation of these alkaloids on silica-based RPLC stationary phases was successfully conducted by the addition of BMIM[BF4] in an acetonitrile:phosphate-buffer-based mobile phase in a pH range of 2.3–5.2. The presented chromatographic method can be used as alternative for monitoring studies or pharmacokinetic application necessary for the evaluation of tobacco smoke exposure. © 2023 by the authors.