The introduction of larger and heavier aircraft with more complex wheel configurations is making the current design methods inadequate for airfield pavements. In addition, airport pavements experience significant wander. However, the effect of wander on airport pavement performance has not been evaluated. In previous studies, the stress interactions between each tire of a triple-dual-tandem (TDT) axle used on B-777 and A380 aircraft cannot be captured using a two-dimensional model. In addition, many of these studies have assumed a linear-elastic material behavior of the pavement layers. The purpose of this study is to conduct a three-dimensional finite element analysis to quantify and evaluate the effects of wander and aircraft wheel configurations on the mechanical response of the pavement layers. The flexible pavement system that is modeled in this study is comprised of a medium and low strength subgrade. The stress-strain response of the base, subbase, and subgrade layers are simulated using an elasto-plastic model and the asphalt layer is modeled separately as a viscoelastic and elasto-plastic material. The model parameters are validated using results from laboratory and field tests. The results of the study show how flexible airport pavements are affected when wander and complex gear configurations are considered. Correlations between deformations from a single wheel and 4- and 6- wheel configurations are also studied to understand the effect of gear configuration on flexible airport pavements. Where possible, the results from the analysis are also compared against full scale results available from the National Airport Pavement Test Facility (NAPTF).