In the present study, the effect of polydopamine coated multi-walled carbon nanotube (PCNT) on the surface properties -wettability and surface free energy (SFE)of a proton exchange membrane (PEM) nanocomposite based on sulfonated poly(ether ether ketone) (SPEEK) was studied. First, the polydopamine (PDA) coating process was optimized based on a response surface methodology (RSM), then PCNTs and the prepared PEM nanocomposites were characterized using field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), UV-vis spectroscopy, X-Ray diffraction (XRD), differential scanning calorimetry (DSC), and atomic force microscopy (AFM) analyses. The physicochemical properties of membranes were also studied. The surface properties of PEMs were evaluated through estimating the SFE based on Owens, Wendt, Rabel, and Kaelble (OWRK) and Kwok and Neumann (K&N) theories; the SFE data revealed that OWRK is a more reliable method in this respect. Interestingly, the total SFE of SPEEK/PCNT nanocomposite did not notably change compared to the SPEEK membrane, but the polarity of SPEEK/PCNTs significantly decreased from 32.1% in SPEEK to 3.8% in the nanocomposite. This result could be attributed to the acid-base interaction of nanofiller and polymer, resulting in the involvement of polar group of polymer and new orientation of SPEEK chains at the surface of the nanocomposite.