Numerical simulation of chloride diffusion through high-performance binding systems such as limestone-calcined clay cement (LC3) and its comparison to control and fly ash modified concretes is discussed. The simulation framework considers the pore structure of concrete, the concentration-dependence of diffusion coefficient, and Freundlich binding. The LC3 concrete and the companion fly ash concrete exhibit similar service lives (~8× control mixture), despite the LC3 system having a reduced clinker factor than the fly ash concrete (~0.5, as opposed to 0.7). The diffusion model is augmented with a scalar isotropic damage variable that accounts for random distribution of microcracks under fatigue loading (e.g., in a bridge deck). The impact of damage on service life at different stress levels, for the different concretes is elucidated. The modeling approach can be used to evaluate the influence of binder composition and damage on effective service life of chloride-exposed concrete structures, thereby aiding in binder selection.