This paper presents a sum of squares (SOS) approach for active fault tolerant control (AFTC) of nonlinear polynomial systems. A polynomial adaptive fault estimation algorithm for polynomial systems is firstly proposed. Then, sufficient conditions for the existence of the fault estimator are given in terms of SOS which can be numerically (partially symbolically) solved via the recently developed SOSTOOLS. Based on the obtained online fault estimation information, a fault-tolerant control strategy is designed for both compensating the effect of actuator faults in real time and stabilizing the closed-loop system. Finally, tunnel diode circuit and mass-spring-damper systems are used to demonstrate the applicability of the proposed approach.