Loss of control is considered as the primary cause of fatal accidents in aviation, which occurs when the aircraft has left the safe flight envelope. To reduce loss-of-control-related accidents, it is important to estimate the safe flight envelope at the current flight condition and integrate it into flight control system design. This task is known as envelope estimation and protection. This project investigates this task on the Innovative Control Effectors aircraft, an over-actuated tailless fighter aircraft with complex aerodynamic coupling between control effectors. It has been observed that this aircraft can easily steer outside the flight envelope and lose control due to its huge control authority. This thesis proposes a novel and practical framework for safe flight envelope estimation and protection, in order to reduce loss-of-control-related accidents. Despite that multiple envelope estimation methods exist in literature, conventional analytical estimation methods fail to function efficiently for systems with high dimensionality and complex dynamics, which is often the case for high-fidelity aircraft models. In this way, this paper develops a probabilistic envelope estimation method based on Monte Carlo simulation. This method generates a probabilistic estimation of the flight envelope with kernel density estimation by simulating a sample of flight trajectories with extreme control effectiveness, which describes the envelope more practically with fuzzy sets instead of conventional crisp sets. It is shown that this method can significantly reduce the computational load compared with previous optimization-based methods and guarantee feasible and conservative envelope estimation of no less than seven dimensions. This method was applied to the Innovative Control Effectors aircraft developed by Lockheed Martin. The estimation results are demonstrated by comparing different flight conditions and covariance analysis. The estimated probabilistic flight envelope is used for online envelope protection by a database approach, which estimates the flight envelope offline and carries the results onboard for protection. Both a conventional state-constraint-based and a novel predictive probabilistic flight envelope protection systems were implemented on a multi-loop nonlinear dynamic inversion controller by extending the concept of pseudo control hedging. No systematic framework was available to apply envelope protection to such controller. Real-time simulation results prove that the proposed framework can protect the aircraft within the estimated envelope and save the aircraft from maneuvers that otherwise would result in loss of control. Possibilities were also explored to employ parametric models in envelope protection to simplify the database. This work, however, is still limited to offline estimation with open-loop commands. Future work can extend this framework to aircraft damage models and closed-loop commands.