A controller is proposed for the robust backstepping control of a class of nonlinear multiple-input multiple-output (MIMO) systems which can be converted to a strict feedback form. The proposed robust backstepping control scheme follows a systematic procedure for the design of control laws and uses time delay estimation (TDE) to estimate the uncertainties such as parameter variations, unknown disturbances, and unmodeled dynamics, etc. The proposed controller can be also applied to nonlinear MIMO systems with unmatched uncertainties. Stability analysis of the closed-loop system which contains the plant and the proposed controller is also studied and hereby a sufficient stability condition for the closed-loop system is proposed. The simulation results show that the control scheme works well with uncertainties and the proposed stability condition is valid. The controller is experimentally verified on a single-link flexible arm to show the effectiveness of the proposed scheme in the complicated systems with uncertainties.