The ratio of citric acid to D-isocitric acid can be used to distinguish authentic and adulterated fruit juices. To separate DL-isocitric acid enantiomers, we used ligand exchange CE. D-Quinic acid was used as a chiral selector ligand and Mn(II), Fe(III), Co(II), Ni(II), Cu(II), and Zn(II) ions were used as the central ions of the chiral selector in the BGE. DL-Isocitric acid was found to be enantioseparated with the above metal ions except for Mn(II) ion. The optimum running conditions for the analysis of D- and L-isocitric acids along with citric acid, an isomer of isocitric acid, were found to be a BGE (pH 5.0) containing 30% ACN, 20 mM acetic acid, 20 mM NiSO4, and 80 mM D-quinic acid. Under these conditions, DL-isocitric and citric acids in fruit juices were analyzed successfully.