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Using modern methods of quantum chemistry, a theoretical substantiation of the high cis-stereospecificity of 1,3-butadiene polymerization catalyzed by the neodymium-based Ziegler–Natta system was carried out. For DFT and ONIOM simulation, the most cis-stereospecific active site of the catalytic system was used. By analyzing the total energy, as well as the enthalpy and Gibbs free energy of the simulated catalytically active centers, it was found that the coordination of 1,3-butadiene in the trans-form was more favorable than in the cis-form by 11 kJ/mol. However, as a result of π-allylic insertion mechanism modeling, it was found that the activation energy of cis-1,3-butadiene insertion into the π-allylic neodymium–carbon bond of the terminal group on the reactive growing chain was 10–15 kJ/mol lower than the activation energy of trans-1,3-butadiene insertion. The activation energies did not change when both trans-1,4-butadiene and cis-1,4-butadiene were used for modeling. That is, 1,4-cis-regulation was due not to the primary coordination of 1,3-butadiene in its cis-configuration, but to its lower energy of attachment to the active site. The obtained results allowed us to clarify the mechanism of the high cis-stereospecificity of 1,3-butadiene polymerization by the neodymium-based Ziegler–Natta system.