The growing interest in application of ionic liquids (ILs) in analytical chemistry has been observed. The aim of presented investigation was to verify whether ILs would be a suitable modifier of the background electrolyte (BGE) for pharmaceutical analysis of the closely related drug analogues. The study demonstrates the use of 1-ethyl-3-methylimidazolium tetrafluoroborate (1E-3MI-TFB) ionic liquid as modifiers in the separation of nicotinic acid and its structural isomers by capillary electrophoresis. Dependences of the ionic liquid concentration in a BGE on the separation parameters like migration time, resolution factor and width at peak's baseline have been compared. The separation mechanism involves the free imidazolium ions, which can interact with inner surface of the capillary wall. Increased 1E-3MI-TFB concentration to 150 mmol/L caused decrease of migration times of analytes, improve peaks shape and increase of separation performances. At this ionic liquid concentration in a BGE resolution factor between nicotinic and isonicotinic acids increased to 1.86. The proposed CE separation procedure is highly reproducible and can be applied in qualitative and quantitative analysis of carboxylic acids.