New electrode material was synthesized via in situ simultaneous-thiol-treatment (STT) of graphene oxide (GO) and polyaniline nanofibers (Pnf), using a small percent of (3-Mercaptopropyl) trimethoxysilane (MPT) as the thiol precursor, during the process of polymerization in high acidic environment. The measured XRD and FTIR spectra confirmed the enhancement of the Pnf binding without impairing its conjugation, and the reduction of GO via chemical modification of the hydroxyl and epoxide groups. The thiolated Pnf-GO system was also characterized by EDX, SEM and TEM, and the results showed a well dispersive porous structure as well as an increase in the surface area over the non-thiolated Pnf-GO system by a factor of 2. Electrochemical studies revealed a well-defined redox peak, suggesting high faradaic contribution. The results of the performed different electrochemical tests agreed on the improvement of the specific capacity and the reduction of the charge-transfer resistance, which were facilitated by the morphological structure of the thiolated Pnf-GO nanocomposite system. A modified Randles equivalent circuit succeeded to model the impedance spectrum of the new electrode system by adding a finite-length Warburg element to account for the highly porous nanoscale structure and the randomly aligned diffusion boundaries.