This paper investigates the problem of robust fault-tolerant containment control for a class of multiagent systems in which multiple active leaders and linear heterogeneous follower subsystems with mismatched affine uncertainties and actuator faults are distributed on a communication network. It first introduces a group of distributed adaptive intermediate estimators, based on which each following agent can estimate the desired containment trajectory objective. Then, by utilizing adaptive parameter estimation approach and S-procedure technique, a decentralized fault-tolerant tracking control algorithm is designed to guarantee all practical states of followers asymptotically track the desired containment trajectory even in the case of actuator faults and heterogeneous affine uncertainties. Interestingly, the main advantage of proposed fault-tolerant containment strategy is that, not only the faulty information from follower subsystems cannot affect neighbor agents, but also both actuator faults and heterogeneous affine uncertainties can be compensated in local subsystem. Finally, a numerical example is given to illustrate the effectiveness of the designed containment control protocol.