The polypyrrole/acetonitrile solution interface was investigated by molecular dynamics simulation for different oxidation states of the polymer in presence of 0.1N lithium perchlorate. The polypyrrole film, acetonitrile and lithium ions were modeled with atomic resolution. From simulation, it was evidenced how the polypyrrole oxi/reduction process is mainly governed by an anionic mechanism, although cations (lithium ions) also play a significant role in the process. Thus, during the polypyrrole reduction process, lithium ions penetrated into the polymeric matrix to compensate the perchlorate ions that were trapped in the polypyrrole matrix due to its low translational diffusion coefficient. In this process, stable ion-pair lithium–perchlorate structures are generated that remain stable along the whole simulations. In addition, during the oxidation process, a polypyrrole swelling was observed. In this regard, the formation of small pores of 4±1Å in the polypyrrole oxidized structure was evidenced and an electrolyte desolvation was obtained during the ion penetration into the polymer matrix associated to the doping process of the polymer. Finally, a diminution in one order of magnitude in the translational diffusion coefficient of perchlorate and lithium ions inside the polymer was estimated compared with bulk solution.