This paper proposes a new guidance and control system for a re-entry vehicle. The vehicle flying through an extensive flight region can be expressed as a nonlinear system which has uncertain dynamic characteristics and physical constraints. In addition, to address considerations of mission abort and changes of landing site during a space transportation mission, sequentially generating flight trajectories from the guidance system is desirable. Therefore, in this study, we attempt to derive an online trajectory generation system by solving a two-point boundary value problem using the concept of flatness as an extension of exact linearization. Moreover, an attitude control system is designed to track a command signal corresponding to a generated trajectory. The system is employed as a constrained adaptive backstepping control method that can accommodate uncertain dynamic characteristics and physical constraints of a re-entry vehicle. The numerical simulations verify the effectiveness of the proposed guidance and control system.