In the last decade, the increasing use of NanoSats and CubeSats has made the re-entry capsule an emerging research field needing updates in configuration and technology. In particular, the door to advancements in terms of efficiency and re-usability has been opened by the introduction of inflatable and/or deployable aerodynamic brakes and the use of on-board electronics for active control. Such technologies allow smaller sizes at launch, controlled re-entries, and safe recovery. This paper deals with the design of a guidance and control algorithm for the re-entry of a capsule with a deployable aero-brake. A trajectory optimization model is used both in the mission planning phase to design the reference re-entry path and during the mission to update the trajectory in case of major deviations from the prescribed orbit, thanks to simplifications aimed at reducing the computational burden. Successively, a trajectory tracking controller, based on Nonlinear Model Predictive Control (NMPC), is able to modulate the opening of the aero-brake in order to follow the planned trajectory towards the target. A robustness analysis was carried out, via numerical simulations, to verify the reliability of the proposed controller in the presence of model uncertainties, orbital perturbations, and measurement noise.