Stereoselective resolution of (R,S)-carprofen methyl ester (CPOMe) by lipase-catalyzed hydrolysis to (S)carprofen (CP) was investigated in an aqueous medium. With the highest catalytic activity, Candida antarctica Lipase A (CALA) was selected as catalyst compared with eight other lipases. Hydroxyethyl-β-cyclodextrin (HE-β-CD) was added to enhance the solubility of (R,S)-CPOMe, which significantly raised the conversion of substrate from 11.12% to 30.84%. Response surface methodology (RSM) was adopted to evaluate the influence of factors on the substrate conversion (c) and enantiomeric excess of product (ee p ), such as pH, concentrations of enzyme and HE-β-CD, temperature, substrate loading, and reaction time. The optimal conditions were obtained, including pH 6.0, 40 mg/mL CALA, 0.05 mmol substrate, 35 mmol/L HE-β-CD, agitation speed of 600 rpm, temperature of 76 °C, and reaction time of 30 h. Under the above conditions, (S)-CP as the desired product was obtained with an enantiomeric excess of 96.24% and overall conversion of 46.07%.