Coating uniformity requirement is becoming more severe as new products come into the market. Coating processes have to be designed not only based on the steady-state operation but also taking into account how the flow responds to ongoing disturbances on process conditions. These disturbances may lead to thickness variation on the deposited liquid layers that may be unacceptable for product performance. This study extends available transient analysis of single-layer slot coating to determine the amplitude of the oscillation of each individual coated layer in two-layer slot coating process in response to small periodic perturbation on different operating parameters. The predictions were obtained by solving the complete transient Navier-Stokes equations for free surface flows. The results show the most dangerous perturbations and how the deposited film thickness variations of each layer can be minimized by changing the geometry of the die lip and liquid viscosities.