The intrinsic properties and structural construction of active materials are crucial to improving the performance of electrodes. Herein, flexible and hydrophilic polyetherimide/polyaniline (PEI/PANI) conductive microfiber membranes with unique core-shell architecture were prepared via electrospinning followed by in-situ chemical oxidation polymerization of aniline doped with 2-acrylamido-2-methyl-1-propanesulfonic acid, and used to boost the properties through the combined action of the pseudocapacitive PANI and abundant porous PEI membranes. For achieving excellent PEI/PANI microfiber membranes as free-standing electrodes, the polymerization time was controlled to refrain from exceed PANI particles agglomeration and maintain the unique three-dimensional porous network structure. Optimized PEI/PANI microfiber membranes with the polymerization time of 7 h presented the best electrochemical properties with high specific capacitance of 249.5 F g−1 at 1 A g−1 and low charge-transfer resistance of 8.316 Ω. Ascribing to the combined effect between the unique pore structure of PEI microfiber membranes and pseudocapacitance of PANI, the flexible supercapacitor based on PEI/PANI-7 demonstrated exceptional capacitance (175.1 F g−1 at 1 A g−1), high energy density (43.4 Wh kg−1) and power density (34.0 kW kg−1), and outstanding flexibility while preserving the cyclic stability. Therefore, this free-standing PEI/PANI microfiber membranes could be deemed as a prospective electrode contender for flexible supercapacitor applications.