In the field of roll-to-roll manufacturing, the accurate prediction and elimination of the tension disturbance in a flexible web are critical because of the unexpected deformation occurring in the roll-to-roll process. Although the causes of the tension error have been examined, no analytical models have been developed to estimate the tension disturbances in an industrial roll-to-roll process accurately. In this article, an advanced model was developed to determine the tension disturbances caused by the run-out arising from the axis mismatch, roundness error, and unbalance, and the velocity variation of the rollers on an industrial-scale roll-to-roll printing process. The estimation performance of the developed model was experimentally verified, and a high average accuracy of 92.4% was attained. Finally, the model was used to determine the maximum permissible run-out caused by the axis mismatch, roundness error, and unbalance of the roller in an industrial-scale roll-to-roll printing process. This model can be universally used to troubleshoot the tension disturbances in roll-to-roll multilayer printing and functional film manufacturing processes and, thereby, facilitate the mass production of highly integrated flexible and foldable electronics.