This paper presents a robust real-time aircraft health monitoring framework using a machine learning based approach, specifically the multivariate Gaussian mixture model (mGMM), for the detection of in-air operational anomalies of an aircraft system. Sensor fusion and noise filtering algorithms have also been adopted to reduce dimensionality of the feature space while avoiding the elimination of useful information from the original flight data. Random noise in each feature, induced by the aircraft sensors and data acquisition system, is filtered out using a weighted averaging window while maintaining inherent variances. The filtered dataset is then fused according to the underlying physics of each sensed feature to reduce redundant features and subsequently trained using the mGMM. The methodology allows monitoring the behavior of each feature as well as correlations between features, significantly improving detection sensitivity. The high computational efficiency of this approach permits real-time monitoring of an aircraft system.