The process of charging and discharging of lithium-ion batteries results in the periodic intercalation and ejection of lithium ions in the anode material. High-capacity anode materials that are of significant interest for next-generation batteries, such as silicon, undergo large deformation during this process. The ensuing electro-chemo-mechanical stresses and accompanying microstructural changes lead to a complex state of inelastic deformation and damage in the silicon electrode that causes a significant capacity loss within just a few cycles. In this study, we attempt to understand, from an atomistic viewpoint, the mechanisms underlying the plasticity behavior of Si-anode as a function of lithiation. Conventional molecular dynamics simulations are of limited use since they are restricted to loading rates in the order of 108 s−1. Practical charging-discharging rates are several orders of magnitude slower, thus precluding a realistic atomistic assessment of the highly rate-dependent mechanical behavior of lithiated silicon anodes via conventional molecular dynamics. In this work, we use a time-scaling approach that is predicated on the combination of a potential energy surface sampling method, minimum energy pathway, kinetic Monte Carlo, and transition state theory, to achieve applied strain rates as low as 1 s−1. We assess and compare the atomistic mechanisms of plastic deformation in three different lithium concentration structures: LiSi2, LiSi, and Li15Si4 for various strain-rates. We find that the strain rate plays a significant role in the alteration of the deformation and damage mechanisms including the evolution of the plastic deformation, nucleation of shear transformation zone, and void nucleation. Somewhat anomalously, LiSi appears to demonstrate (comparatively) the least strain rate sensitivity.