Most current modeling techniques assume that pavement layers are homogeneous. This assumption can be considered one of the main sources of uncertainty in the performance of pavement structures. The main objective of this paper is to present a methodology that includes the uncertainty of material properties as part of the mechanical response of pavement structures. This methodology efficiently combines a stochastic technique with finite-element modeling. The capabilities of the proposed method are illustrated by studying the role of the internal air void distribution of asphalt mixtures on the mechanical performance of flexible pavements. The results from this model corroborate its usefulness to incorporate variability in the mechanical analysis of pavements. Particularly, the methodology was effective in reproducing internal void distributions observed in compacted asphalt layers in the field and its ability to include such distributions in the macromechanical modeling of flexible pavements.