For the purposes of this paper, the National Airspace System (NAS) encompasses the operations of all aircraft which are subject to air traffic control procedures. The NAS is a highly complex dynamic system that is sensitive to aeronautical decision-making and risk management skills. In order to ensure a healthy system with safe flights a systematic approach to anomaly detection is very important when evaluating a given set of circumstances and for determination of the best possible course of action. Given the fact that the NAS is a vast and loosely integrated network of systems, it requires improved safety assurance capabilities to maintain an extremely low accident rate under increasingly dense operating conditions. Data mining based tools and techniques are required to support and aid operators’ (such as pilots, management, or policy makers) overall decision-making capacity. Within the NAS, the ability to analyze fleetwide aircraft data autonomously is still considered a significantly challenging task. For our purposes a fleet is defined as a group of aircraft sharing generally compatible parameter lists. Here, in this effort, we aim at developing a system level analysis scheme. In this paper we address the capability for detection of fleetwide anomalies as they occur, which itself is an important initiative toward the safety of the real-world flight operations. The flight data recorders archive millions of data points with valuable information on flights everyday. The operational parameters consist of both continuous and discrete (binary & categorical) data from several critical subsystems and numerous complex procedures. In this paper, we discuss a system level anomaly detection approach based on the theory of kernel learning to detect potential safety anomalies in a very large data base of commercial aircraft. We also demonstrate that the proposed approach uncovers some operationally significant events due to environmental, mechanical, and human factors issues in high dimensional, multivariate Flight Operations Quality Assurance (FOQA) data. We present the results of our detection algorithms on real FOQA data from a regional carrier.