A synchronous control system for dual parallel stages is proposed in order that the synchronous error owing to the skew disturbances can be quickly and stably eliminated. The control system is composed of two disturbance observers and a synchronous controller. The two disturbance observers are designed to decrease the mismatched dynamics between a nominal model and a real plant with nonlinear properties and to reject instantly disturbances for each stage. The synchronous controller is designed from the view point of accurate synchronization and improvement of damping characteristics for the synchronous control system. The proposed synchronous control system is evaluated and compared experimentally with a normal cross-coupling control system without disturbance observer. The experiment results show that the new control system considerably reduces the synchronous error against skew disturbances. In addition, the synchronous error can be quickly and more stably eliminated through the improvement of the damping characteristics of the synchronous control system using a PD compensator.