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A method to determine aceclofenac, ketorolac, and sulindac in human urine samples using microemulsion electrokinetic chromatography (MEEKC) has been developed in this study. The optimization of MEEKC conditions was carried out by changing the microemulsion compositions including the buffer pH, borate salt concentration, surfactant concentration, co-surfactant concentration, organic modifier concentration, and oil droplet concentration. The optimum separation of selected drugs was obtained with a composition of microemulsion containing 10 mM borate buffer pH 9, 0.5% sodium dodecyl sulphate (SDS), 6.6% n-butanol, 6.0% acetonitrile, and 0.8% ethyl acetate. Excellent linearity was obtained in the range concentration of 25 to 200 ppm with r2 > 0.999. Limits of detection (LOD, S/N = 3) and limits of quantification (LOQ, S/N = 10) were 2.72 to 4.75 and 9.08 to 15.85 ppm, respectively. The solid-phase extraction (SPE) method using C-18 as an adsorbent and the solid phase micro-tip extraction (SPMTE) method using multiwalled carbon nanotubes (MWCNTs) as an adsorbent were used to clean-up and pre-concentrate the urine samples prior to the MEEKC analysis. The best recoveries of the selected drugs in the spiked urine sample were 91 to 103% with RSD of 1.26 to 4.03% (n = 3) using the SPE-MEEKC method.