By wrapping a porous membrane around the coated stir bar, a novel membrane protected stir bar sorptive extraction (MPSBSE) was proposed to filter out the high molecular weight interferences (such as humic acid), resulting in the analysis of real environmental water samples without filtration or centrifugation. Hydrophilic and hydrophobic membranes were compared and hydrophobic polytetrafluoroethylene (PTFE) membrane impregnated with methanol was employed to protect the C18 coated stir bar. The impregnated methanol improves the transfer of target analytes from sample solution to the pores and lumen of the membrane, and then to the coated stir bar inside. By combining C18-MPSBSE with HPLC-UV, a method was proposed for the direct determination of two common non-steroidal anti-inflammatory drugs, Ketoprofen (KEP) and Naproxen (NAP) in complex water samples. Under the optimized conditions, the limit of detections of KEP and NAP are 7.89, 9.52μgL−1 in the waste water and 7.69, 6.90μgL−1 in the pure water, respectively, with the enrichment factors of 32.0–49.1-fold. Besides, the lifetime of the prepared C18 stir bar protected by PTFE membrane (50 times) is longer than that of C18 stir bar without membrane protection (20 times), indicating that the friction damage of SBSE coating during extraction was effectively avoided. The developed method was successfully applied to the analysis of KEP and NAP in domestic sewage and campus lake water samples.