Utilization of core-shell rather than monometallic nanocrystals (NCs) facilitates fine-tuning of NC properties for applications. However, compositional evolution via intermixing can degrade these properties prompting recent experimental studies. We develop an atomistic-level stochastic model for vacancy-mediated intermixing exploiting a formalism which allows incorporation at an ab initio density functional theory level of not just the thermodynamics of vacancy formation, but also relevant diffusion barriers for a vast number of possible local environments (in the core and in the shell, at the interface, and in the intermixed phase). This facilitates a predictive treatment and comprehensive understanding of intermixing on the relevant time scale (e.g., 101-103 s). In contrast, previous modeling at the atomistic level utilized only unrealistic generic prescriptions of barriers or employed simplified continuum treatments. For Au@Ag octahedral core-cubic shell NCs, our modeling not only captures the experimentally observed rate or time scale for intermixing of ∼100 s at 450 °C for 60 nm NCs, but also elucidates the underlying rate controlling processes and the effective intermixing barrier.