The morphological control of proton conductive nanofibrous mat used in proton exchange membranes (PEMs) is a key issue to improve proton conductivity of PEMs. In this study, response surface methodology (RSM) was utilized to investigate the morphological characterizations of electrospun sulfonated poly (ether ether ketone) (SPEEK) nanofibrous membranes. The effects of electrospinning parameters namely solution concentration, applied voltage and tip to collector distance were studied on the average diameter, its standard deviation and the degree of alignment of SPEEK nanofibers. The adequacy of the response surface models was verified by the validation experiments. Optimized conditions were obtained to meet the desired status of collecting more uniform and finer nanofibers with improved alignment. After obtaining the significant factors and optimal test level, an additional optimization was conducted at different take-up speeds to fabricate high-grade aligned nanofibers. The resultant nanofibers had the diameter of 107 +/- 22 nm at the optimum point which was in good agreement with the predicted response values. The highest degree of alignment was yielded at the take-up speed of 8.8 m/s with the maximum second-order orientation parameter of 0.869. Electrochemical spectroscopy analysis showed that the aligning of proton conductive nanofibers improved in-plane proton conductivity about 67%. POLYM. ENG. SCI., 2017. (c) 2017 Society of Plastics Engineers