In this article, the distributed adaptive fixed-time output time-varying formation tracking issue of heterogeneous multiagent systems (MASs) with actuator faults is addressed, in which the followers suffer from loss-of-effectiveness actuator faults, and the leader has unknown bounded input. To solve the above issue, a distributed fixed-time observer is constructed with the leader’s unknown input, by which each follower can obtain the leader’s states in a predesigned time. Then, based on the observer and the desired formation vector, a local adaptive fixed-time fault-tolerant formation control algorithm is proposed for each follower with the help of time-varying gains to make up for the influence of actuator faults. Furthermore, it is proven that the designed controller can satisfactorily accomplish the considered task of the heterogeneous MASs by using the Lyapunov stability theory. Specifically, the obtained upper bound of the convergence time only depends on a few controller parameters. Finally, a simulation example is implemented to validate the efficiency of the analytical results.