In this paper, a novel adaptive fault‐tolerant control (FTC) scheme is proposed for a class of flexible air‐breathing hypersonic vehicles with unknown inertial and aerodynamic parameters and even input constraints. The fault model under consideration covers the case that all actuators suffer from unknown time‐varying faults. In the controller design and stability analysis, we introduce new Lyapunov functions, some differentiable auxiliary functions, a bound estimation approach, and a Nussbaum function, which help us successfully circumvent the obstacle caused by the faults, input constraints, and flexible modes. In addition to higher reliability, the proposed scheme is able to ensure that all closed‐loop signals are globally uniformly bounded and to steer the tracking errors of altitude and velocity into predefined arbitrarily small residual sets. As a result, the tracking accuracy can be designated in advance. Simulation results illustrate the effectiveness of the proposed scheme.