The pavements of the Beijing Capital International Airport (BCIA), China, where a buried fault zone lies beneath, have undergone continuous severe damages since 2008, but its causes remain unclear. This study focuses on the combined effect of moving aircraft loads and a buried fault zone existence, considering the enormous number of airport operations at the BCIA and the complex conditions of the pavement structure. Hence, a series of numerical simulations conducted using the three-dimensional finite element model were performed. Two models were developed in this study. Model 1 contained a buried fault zone, whereas model 2 did not. The simulation scenarios in each model include a low-speed scenario (scenario 1), a moderate-speed scenario (scenario 2), and a high-speed scenario (scenario 3). Our results show that the most evident deflections caused by the aircraft loads were largely concentrated on the pavements built on the fault zone. The maximum vertical displacement after loading once in model 1 was determined as 0.5 ~ 0.7 mm, whereas in model 2 was 0.4 ~ 0.5 mm. The greatest vertical displacements were generated in scenario 1 rather than in scenario 3, in both models 1 and 2. Moreover, the maximum shear strains on the pavement surface in model 1 are about 2 ~ 19 times larger than in model 2. These findings suggest that aircraft moving loads in the BCIA, especially the low-speed loads, contributed a lot to the recurrent pavement faulting and demonstrate the adverse effects of the buried fault zone on pavement performance.