In this study, a dynamical adaptive integral backstepping variable structure control (DAIBVSC) system based on the Lyapunov stability theorem is proposed for the trajectory tracking control of a nonlinear uncertain mechatronic system with disturbances. In this control scheme, no prior knowledge is required on the uncertain parameters and disturbances because it is estimated by two types of dynamical adaptive laws. These adaptive laws are integrated into the dynamical adaptive integral backstepping control and variable structure control (VSC) parts of the DAIBVSC. The dynamical adaptive law in the dynamical adaptive integral backstepping control part updates parametric uncertainties, while the other in the VSC part adapts upper bounds of non-parametric uncertainties and disturbances. In order to achieve a more robust output tracking and better parameter adaptation, the control system is extended by one integrator and sliding surface is augmented by an integral action. Experimental evaluation of the DAIBVSC is conducted with respect to performance and robustness to parametric uncertainties. Experimental results of the DAIBVSC are compared with those of a traditional VSC. The proposed DAIBVSC exhibits satisfactory output tracking performance, good estimation of the uncertain parameters and can reject disturbances with a chattering free control law. Copyright (c) 2017 John Wiley & Sons, Ltd.