In this paper we consider the problem of constraint handling for an airbreathing hypersonic vehicle (HSV) through a hierarchical control architecture. A reference manager is incorporated as an intermediate control loop whose role is to modify an offline generated reference trajectory, without knowledge of disturbances, to enforce state and input constraints. Compared with traditional constraint handling approaches in HSV literature, this proposed approach allows for the deployment of controllers that are not typically formulated to handle constraints. We provide a computation time and constraint management comparison between a scheme that directly utilizes the nonlinear vehicle model and one that performs online linearization of the model.