The enantiomeric separation of 9-fluorenylmethoxycarbonyl chloride (FMOC)-homocysteine (Hcy) by CE was investigated using gamma-CD and the chiral ionic liquid (R)-(1-hydroxybutan-2-yl)(trimethyl)azanium-bis(trifluoromethanesulfon)imidate (also called (R)-N,N,N-trimethyl-2-aminobutanol-bis(trifluoromethane-sulfon)imidate) (EtCholNTf(2)) as chiral selectors. Using 2 mM gamma-CD and 5 mM EtCholNTf(2) in 50 mM borate buffer (pH 9), FMOC-Hcy enantiomers were separated with a resolution value of 3.8. A reversal in the enantiomer migration order in comparison with the single use of gamma-CD in the separation buffer was obtained. Then, NMR experiments were carried out to elucidate the interactions taking place in the enantiomeric separation of FMOC-Hcy. NMR analyses highlighted the formation of an inclusion complex since the hydrophobic group of FMOC-Hcy was inserted into the gamma-CD cavity. Moreover, interactions between EtCholNTf(2) and gamma-CD were also observed, suggesting that the chiral ionic liquid would also enter the cavity of the gamma-CD.