Flow-induced vibration (FIV) is a design concern in many engineering applications such as tube bundles in heat exchangers. When FIV materializes, it often results in fatigue and/or fretting wear of the tubes, leading to their failure. Three cross-flow excitation mechanisms are responsible for such failures: random turbulence excitation, Strouhal periodicity, and fluidelastic instability. Of these three mechanisms, fluidelastic instability has the greatest potential for destruction. Because of this, a large amount of research has been conducted to understand and predict this mechanism. This paper presents a time domain model to predict the fluidelastic instability forces in a tube array. The proposed model accounts for temporal variations in the flow separation. The unsteady boundary layer is solved numerically and coupled with the structure model and the far field flow model. It is found that including the boundary layer effect results in a lower stability threshold. This is primarily due to a larger fluidelastic force effect on the tube. The increase in the fluidelastic effect is attributed to the phase difference between the boundary layer separation point motion and the tube motion. It is also observed that a non-linear limit cycle is predicted by the proposed model.