Safe autonomous operations of an Unmanned Aerial System (UAS) requires that the UAS can react to unforeseen circumstances, for example, after a failure has occurred. In this paper we describe a model-based run-time architecture for autonomous on-board diagnosis, system health management, and contingency management. This architecture is being instantiated on top of NASA's Core Flight System (cFS/cFE) as amajor component of the on-board AutonomousOperating System (AOS). We will describe our diagnosis and monitoring components, which continuously provide system health status. Automated reasoning with constraint satisfaction form the core of our decision-making component, which assesses the current situation, aids in failure disambiguation, and constructs a contingency plan to mitigate the failure(s) and allow for a safe end of the mission. We will illustrate our contingency management system with two case studies, one for a fixed-wing aircraft in simulation, and one for an autonomous DJI S1000+ octo-copter.