In this paper, a fault-tolerant control scheme is proposed for a class of single-input and single-output non-linear systems with the unknown time-varying system fault and the dead-zone. The non-linear state observer is designed for the non-linear system using differential mean value theorem, and the non-linear fault estimator that estimates the unknown time-varying system fault is developed. On the basis of the designed fault estimator, the observer-based fault-tolerant tracking control is then developed using the backstepping technique for non-linear systems with the dead-zone. The stability of the whole closed-loop system is rigorously proved via Lyapunov analysis and the satisfactory tracking control performance is guaranteed in the presence of the unknown time-varying system fault and the dead-zone. Numerical simulation results are presented to illustrate the effectiveness of the proposed backstepping fault-tolerant control scheme for non-linear systems.