The durability of reinforced concrete structures is closely related to moisture state in cement-based materials. Therefore, it is crucial to develop moisture models that can accurately predict moisture state in the materials. However, many studies reported anomalous moisture transport in cement-based materials that cannot be well simulated by the conventional models. Several reasons have been investigated in the literature, such as the complex pore structure, chemical reactions with water, dimensional changes of the tested specimen, etc. Nevertheless, only a few models are able to capture the anomaly of moisture transport. This study viewed the main moisture transport coefficient—permeability—as a kinetic variable that depends on both the degree of moisture saturation and the contact time. The time-dependence was formulated by the decay (for drying) or growth (for wetting) functions. The saturation-dependence was calculated by the van Genuchten–Mualem (VGM) model. These functions were then implemented into a moisture transport model that was developed in previous studies. The proposed model was validated by experimental data and showed a good agreement for cement pastes that were dried or wetted in the hygroscopic range. Numerical simulation results were also compared with the simplified solutions to a fractional derivative model (FDM) of anomalous diffusion and the empirical Weibull function. We found that the solutions to the FDM cannot provide appropriate results. Weibull function performs as well as the proposed model, but the empirical function lacks physical meanings.