A long flexible material called the web is converted into the final product through various processes such as printing, drying, coating, and laminating using a web handling system. The web is transported from an unwind roller to a rewind roller through some guide and drive rollers in the system. The servo motors control the rollers to regulate their rotation velocity or torque in the system, where web tension and transportation velocity controls play an important role in achieving the high quality of the web product. However, unacceptable variations, such as motor torque pulsation, roller misalignment, and roller eccentricity, cause tension/velocity control performance deterioration. These act on the tension/velocity control system as periodic ripple disturbances. This paper presents a control approach to regulate the web tension and transportation velocity at constant values in the web handling system. An iterative learning control system is designed to identify and suppress periodic ripple disturbances because these disturbances are repeated periodically during web transportation. The learning controller introduces a filter to stabilize the learning process. Furthermore, it is implemented as a zero-phase lowpass filter to improve the phase delay. The effectiveness of the proposed approach has been verified by conducting the experiment using a laboratory prototype of a web handling system.