A novel method has been developed for the on-column labeling of amino acid enantiomers with 9-fluoroenylmethyl chloroformate (FMOC), followed by chiral CE with a binary chiral selector system and UV detection. Efficient labeling was achieved by sequential injection of amino acids, borate buffer, and FMOC labeling solution at 0.2 psi for 6 s. After injection, the sandwich sections were electrically mixed at 250 V/cm. for 6 s and allowed to react (electric field-free) at room temperature for 2 min. With this procedure, successful online-labeling and chiral CE separation of 19 pairs of amino acids (AA) have been conducted, giving 17 pairs fully enantioresolved (R-s = 1.73-5.79) and two pairs partially resolved (Ala, R-s = 0.39 and Arg, R-s = 1.15) using a running buffer of 150 mM borate containing 30 mM P-CD, 30 mM sodium taurodeoxycholate (STDC), and 15% isopropanol (IPA) at pH 9.0. Chiral CE of some mixed pairs was also demonstrated, much the same as using precolumn labeling. Surprisingly, Met, Asp, Asn, Gln, and His gained even higher enantioresolution (up to 2.5%) compared with the case of precolumn labeling. As validated by both artificially prepared solutions and serum samples, the method was applicable to the quantitative determination of AA, with LODs down to 4.0 mu M. The method allowed the determination of D-AA at the ratio of 1:100 (D:L).