The chromatographic retention behaviors of various amino acids were investigated using ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF4]), as a mobile phase additive and a reversed phase C-18 media as a stationary phase. The amino acids investigated include L-tyrosine, N-CBZ-L-tyrosine, L-phenylalanine, N-CBZ-L-phenylalanine, L-methionine, and N-CBZ-L-methionine. The effect of ionic liquid on N-CBZ-L-amino acids was found to be different from that on L-amino acids. As the concentration of ionic liquid in mobile phase increased, the retention factors of L-amino acids showed a decreasing trend, whereas those of N-CBZ-L-amino acids exhibited a minute change. The selectivity between L-amino acid and N-CBZ-L-amino acid was, thus, improved by increasing the content of ionic liquid. In addition, the peak shapes of L-amino acids, if asymmetric, were transformed into symmetric ones by increasing the ionic liquid content. The increase of feed concentration causes the overloaded condition, leading to a decrease in the retention factor. If such effect of feed concentration is coupled with the effect of using ionic liquid, one can achieve a better separation between L-amino acid and N-CBZ-L-amino acid.