Naproxen (NAP)/cellulose acetate hybrid nanofibers were prepared by positive and reversed emitting electrodes electrospinning setups. The morphology and structure of the resultant nanofibers were characterized, and the NAP release behaviors were investigated. It was found that NAP dispersed in the CA matrix in molecular level, and no aggregation and dimers of NAP were found in the resultant NAP/CA hybrid nanofibers due to the formation of hydrogen bonds between NAP and CA. The nanofibers obtained by reversed emitting electrode electrospinning setup have a thicker diameter and a faster NAP release rate compared with those obtained by positive emitting electrode electrospinning setup. The faster drug release of NAP from nanofibers prepared by reversed emitting electrode electrospinning is due to the fact that the concentration of NAP molecules near the surface of the nanofibers is relatively higher than that of the nanofibers prepared by positive emitting electrode electrospinning setup. The effects of the electrode polarity on the distribution of drugs in nanofibers can be used to prepare hybrid electrospun fibers of different drug release rates, which may found applications in biomedical materials.