A study by molecular dynamics (MD) simulation of the acetonitrile diffusion into a polypyrrole film was carried out with atomic detail in a 0.1N lithium perchlorate solution. From the simulated trajectories, the acetonitrile behavior was estimated from bulk solution to the interior of the polypyrrole film, across the polypyrrole/solution interface, for a neutral (reduced) and charged (oxidized) state of the polymer. Among other properties, the translational diffusion coefficient and rotational relaxation time of the acetonitrile were calculated, where a diminution in the translational diffusion coefficient was measured in the interior of the polypyrrole matrix compared to bulk, independently of the oxidation state of the polymer, in contrast with the behavior of the rotational relaxation time that increases from bulk to the interior of the polymer for both oxidation states. In addition, the difference of free energy ΔG associated to the acetonitrile penetration into the polymer was calculated. From the results, it was evidenced that the scarce affinity of acetonitrile to diffuse into the polymer in its reduced state is related with the positive uniform difference of free energy ΔG≈20 kJ/mol, while in the oxidized state, an important free energy barrier of ΔG≈10 kJ/mol has to pass trough for reaching stable sites inside the polymer with values of ΔG up to −10 kJ/mol.