A new energy-based approach is presented for the prediction of rutting performance in flexible pavement systems. The underlying modeling approach is developed based on the thermodynamics of irreversible processes with new state variables introduced to account for the meso-structural changes in the internal structure arrangement due to grain boundary sliding. The model is simplified and implemented in a pavement analysis framework for the evaluation of the model performance in the rutting prediction using a series of well-documented data of well quality controlled WesTrack pavement sections. Densification behavior is observed in measured rutting data during the initial age of each pavement section. A simplified densification model is introduced based on its correlation with in-place air void content. The energy-based plastic model associated with the densification model effectively captured the rutting behavior of all three gradation groups used in the WesTrack project. The result of the analysis shows that the model accurately captures the rutting tendencies observed in flexible pavement sections with decreasing rate of accumulation of plastic deformation over the pavement life due to the aging effects. The mechanism of rutting development can be effectively explained by the present models supported by precise predictions of all the details of initial densification behaviors and seasonal variations during the test period in the WesTrack project.