In this investigation, a new approach was developed to study the influence of cage flexibility on the dynamics of inner and outer races and balls in a bearing. A 3D explicit finite element model (EFEM) of the cage was developed and combined with an existing discrete element dynamic bearing model (DBM) with six degrees of freedom. The EFEM was used to determine the cage dynamics, deformation, and resulting stresses in a ball bearing under various operating conditions. A novel algorithm was developed to determine the contact forces between the rigid balls and the flexible (deformable) cage. In this new flexible cage dynamic bearing model, the discrete and finite element models interact at each time step to determine the position, velocity, acceleration, and forces of all bearing components. The combined model was applied to investigate the influence of cage flexibility on ball-cage interactions and the resulting ball motion, cage whirl, and the effects of shaft misalignment. The model demonstrates that cage flexibility (deflection) has a significant influence on the ball-cage interaction. The results from this investigation demonstrate that the magnitude of ball-cage impacts and the ball sliding reduced in the presence of a flexible cage; however, as expected, the cage overall motion and angular velocity were largely unaffected by the cage flexibility. During high-speed operation, centrifugal forces contribute substantially to the total cage deformation and resulting stresses. When shaft misalignment is considered, stress cycles are experienced in the bridge and rail sections of the cage where fatigue failures have been observed in practice and in experimental studies.