The kinetics of lithium atoms in various Li–Si binary compounds are investigated using density functional theory calculations and kinetic Monte Carlo calculations. The values of the Li migration energy barriers are identified by NEB calculations with vacancy–mediated, interstitial and exchange migration mechanisms in crystalline LiSi, Li12Si7, Li13Si4, and Li15Si4. A comparison of these NEB results shows that the vacancy–mediated Li migration is identified as the dominant diffusion mechanisms in Li–Si compounds. The diffusion coefficients of Li in Li–Si compounds at room temperature are determined by KMC simulation. From the KMC results, the recalculated migration energy barriers in LiSi, Li12Si7, Li13Si4, and Li15Si4 correspond to 0.306, 0.301, 0.367 and 0.320 eV, respectively. Compared to the Li migration energy barrier of 0.6 eV in crystalline Si, the drastic reduction in the Li migration energy barriers in the lithiated silicon indicates that the initial lithiation of the Si anode is the rate-limiting step. Furthermore, it is also found that Si migration is possible in Li–rich configurations. On the basis of these findings, the underlying mechanisms of kinetics on the atomic scale details are elucidated.