Molecularly imprinted polymers (MIPs) of (S)-ketoprofen and (S)-naproxen are prepared using non-covalent imprinting in the presence of template molecules. The prepared MIPs are used as the chiral stationary phase to separate ramemic naproxen and ketoprofen. The results show that racemic naproxen and ketoprofen are efficiently resolved on MIPs. The effect of concentration of acetic acid in the mobile phase is studied, and the data are analyzed using the affinity chromatography model, and the close agreement is achieved between the simulated and experimental curves. The results suggest that the affinity chromatography mechanism controls the retention in this system. Moreover, the affinity chromatography equilibrium constants on (S)-naproxen and (S)-ketoprofen are estimated.