In this work, four ionic liquids differing in the length of the alkyl chain on the imidazolium cation and one ionic liquid containing tetraethylammonium, all with the same counterion, (i.e. 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIm-BF4), 1-butyl-3-methylimidazolium tetrafluoroborate (BMIm-BF4), 1-hexyl-3-methylimidazolium tetrafluoroborate (HMIm-BF4), 1-methyl-3-octylimidazolium tetrafluoroborate (MOIm-BF4), and tetraethylammonium tetrafluroborate (Et4N-BF4)) were tested as mobile phase additives for HPLC separation of a group of seven basic fluoroquinolone (FQ) antibiotics for human and veterinary use (i.e. fleroxacin, ciprofloxacin, lomefloxacin, danofloxacin, enrofloxacin, sarafloxacin, and difloxacin) using a conventional reversed-phase Nova-Pak C18 column. Fluorescence detection was used. Among the ionic liquids selected, use of BMIm-BF4 enabled effective separation of these compounds with relatively low analysis time (14 min). The best separation was achieved by isocratic elution at 1 mL min−1 with 5 mmol L−1 BMIm-BF4 and 10 mmol L−1 ammonium acetate at pH 3.0 with 13% (v/v) acetonitrile. Limits of detection (LODs) for fluorescence detection were in the range 0.5–11 μg L−1. The method was tested by analyzing several water samples after the optimization of a suitable solid-phase extraction (SPE) procedure using Oasis HLB cartridges. Mean recovery values were above 84% for all analytes with LODs in the range 1–29 ng L−1.