In this report, a novel preparation method of molecularly imprinted polymers (MIPs) for CEC was developed. Molecularly imprinted monolithic columns for (S)-ibuprofen were prepared and evaluated, in which charged entities responsible for establishing EOF have been derived from gamma-methacryloxypropyltrimethoxysilane (gamma-MAPS), which was hydrolyzed following copolymerization with 4-vinylpyridine (4-VPY) and ethylene glycol dimethacrylate (EDMA). The EOF and molecular recognition of the stationary phase were investigated in aqueous and nonaqueous media, respectively. The experimental results indicated that the material showed a reasonably stable EOF and the prepared separation materials were capable of separating racemic ibuprofen, a task that could not be accomplished by MIPs prepared in parallel, using methacrylic acid (MAA) as a functional monomer. The efficiency at pH 3.2 for the first-eluted enantiomer and the last-eluted enantiomer (the imprinted analyte) were 128,700 and 2100 plates/m, respectively.